Genetic Variant LOC124904891:n.1272A>G (chr20-35602948-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_007067570.1(LOC124904891):n.1272A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,420 control chromosomes in the GnomAD database, including 5,937 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.27 ( 5928 hom., cov: 30)

Exomes 𝑓: 0.18 ( 9 hom. )

Consequence

LOC124904891
XR_007067570.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0890

Publications

12 publications found

Variant links:

COSMIC-nc: COSV61513974

Genes affected

LOC124904891 (HGNC:):

LOC124904891 links:

FER1L4 (HGNC:15801): (fer-1 like family member 4 (pseudogene)) Predicted to enable metal ion binding activity. Predicted to be involved in plasma membrane organization. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

FER1L4 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904891	XR_007067570.1 link	n.1272A>G		non_coding_transcript_exon_variant	Exon 1 of 2
FER1L4	NR_119376.1 link	n.891+62T>C		intron_variant	Intron 9 of 42

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000293413	ENST00000325076.9 link	n.723+62T>C	intron_variant	Intron 6 of 8	2
ENSG00000293413	ENST00000430275.6 link	n.891+62T>C	intron_variant	Intron 9 of 25	5
ENSG00000293413	ENST00000434843.7 link	n.1025+62T>C	intron_variant	Intron 7 of 9	3

Frequencies

GnomAD3 genomes

AF:

0.268

AC:

40596

AN:

151588

Hom.:

5899

Cov.:

show subpopulations

Gnomad AFR

AF:

0.389

Gnomad AMI

AF:

0.213

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.266

Gnomad EAS

AF:

0.161

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.338

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.273

GnomAD4 exome

AF:

0.183

AC:

131

AN:

714

Hom.:

Cov.:

AF XY:

0.175

AC XY:

AN XY:

418

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.333

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.180

AC:

AN:

488

Middle Eastern (MID)

AF:

0.667

AC:

AN:

European-Non Finnish (NFE)

AF:

0.179

AC:

AN:

168

Other (OTH)

AF:

0.158

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.268

AC:

40669

AN:

151706

Hom.:

5928

Cov.:

AF XY:

0.267

AC XY:

19796

AN XY:

74164

show subpopulations

African (AFR)

AF:

0.390

AC:

16094

AN:

41308

American (AMR)

AF:

0.223

AC:

3406

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.266

AC:

922

AN:

3466

East Asian (EAS)

AF:

0.161

AC:

826

AN:

5140

South Asian (SAS)

AF:

0.349

AC:

1674

AN:

4802

European-Finnish (FIN)

AF:

0.197

AC:

2078

AN:

10554

Middle Eastern (MID)

AF:

0.336

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.218

AC:

14786

AN:

67892

Other (OTH)

AF:

0.281

AC:

592

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1449

2899

4348

5798

7247

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

424

848

1272

1696

2120

<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:

0.257

Hom.:

1110

Bravo

AF:

0.270

Asia WGS

AF:

0.338

AC:

1175

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.2

(source)

DANN

Benign

0.45

PhyloP100

-0.089

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over