Genetic Variant NM_001013627.3:c.586G>A (chrX-72134530-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001013627.3(NHSL2):c.586G>A(p.Glu196Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00495 in 1,165,875 control chromosomes in the GnomAD database, including 262 homozygotes. There are 1,940 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.0054 ( 30 hom., 204 hem., cov: 25)

Exomes 𝑓: 0.0049 ( 232 hom. 1736 hem. )

Consequence

NHSL2
NM_001013627.3 missense

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 2.45

Publications

1 publications found

Variant links:

Genes affected

NHSL2 (HGNC:33737): (NHS like 2) Predicted to enable calcium ion binding activity. Predicted to be involved in cell differentiation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

NHSL2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0015164912).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001013627.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
NHSL2	NM_001013627.3	MANE Select	c.586G>A	p.Glu196Lys	missense	Exon 4 of 8	NP_001013649.2	Q5HYW2-1
NHSL2	NM_001438805.1		c.655G>A	p.Glu219Lys	missense	Exon 5 of 9	NP_001425734.1
NHSL2	NM_001438806.1		c.499G>A	p.Glu167Lys	missense	Exon 4 of 8	NP_001425735.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
NHSL2	ENST00000633930.2	TSL:5 MANE Select	c.586G>A	p.Glu196Lys	missense	Exon 4 of 8	ENSP00000488668.1	Q5HYW2-1
NHSL2	ENST00000510661.2	TSL:1	c.-381G>A		5_prime_UTR	Exon 2 of 3	ENSP00000424079.2	Q5HYW2-2
NHSL2	ENST00000373677.1	TSL:1	n.882G>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.00545

AC:

616

AN:

112996

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000770

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00296

Gnomad ASJ

AF:

0.00677

Gnomad EAS

AF:

0.136

Gnomad SAS

AF:

0.0108

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000375

Gnomad OTH

AF:

0.00393

GnomAD2 exomes

AF:

0.0111

AC:

1245

AN:

112033

AF XY:

0.0105

show subpopulations

Gnomad AFR exome

AF:

0.000316

Gnomad AMR exome

AF:

0.000258

Gnomad ASJ exome

AF:

0.00601

Gnomad EAS exome

AF:

0.137

Gnomad FIN exome

AF:

0.0000862

Gnomad NFE exome

AF:

0.000442

Gnomad OTH exome

AF:

0.00688

GnomAD4 exome

AF:

0.00490

AC:

5156

AN:

1052826

Hom.:

232

Cov.:

AF XY:

0.00505

AC XY:

1736

AN XY:

343674

show subpopulations

African (AFR)

AF:

0.000241

AC:

AN:

24895

American (AMR)

AF:

0.000287

AC:

AN:

27900

Ashkenazi Jewish (ASJ)

AF:

0.00693

AC:

129

AN:

18612

East Asian (EAS)

AF:

0.160

AC:

4328

AN:

27122

South Asian (SAS)

AF:

0.00369

AC:

184

AN:

49835

European-Finnish (FIN)

AF:

0.0000798

AC:

AN:

37598

Middle Eastern (MID)

AF:

0.000980

AC:

AN:

4083

European-Non Finnish (NFE)

AF:

0.000249

AC:

204

AN:

818444

Other (OTH)

AF:

0.00654

AC:

290

AN:

44337

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

168

336

503

671

839

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

144

216

288

360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00543

AC:

614

AN:

113049

Hom.:

Cov.:

AF XY:

0.00580

AC XY:

204

AN XY:

35199

show subpopulations

African (AFR)

AF:

0.000768

AC:

AN:

31239

American (AMR)

AF:

0.00296

AC:

AN:

10818

Ashkenazi Jewish (ASJ)

AF:

0.00677

AC:

AN:

2659

East Asian (EAS)

AF:

0.136

AC:

485

AN:

3563

South Asian (SAS)

AF:

0.0108

AC:

AN:

2768

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6235

Middle Eastern (MID)

AF:

0.00

AC:

AN:

218

European-Non Finnish (NFE)

AF:

0.000375

AC:

AN:

53321

Other (OTH)

AF:

0.00324

AC:

AN:

1545

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00172

Hom.:

Bravo

AF:

0.00658

ExAC

AF:

0.00525

AC:

120

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

Spinocerebellar ataxia, X-linked (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.63

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.13

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.81

MetaRNN

Benign

0.0015

MetaSVM

Benign

-1.1

PhyloP100

2.4

PrimateAI

Benign

0.43

Sift4G

Benign

0.10

Vest4

0.040

ClinPred

0.0072

GERP RS

3.4

PromoterAI

0.0091

Neutral

(source)

gMVP

0.35

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over