Genetic Variant NM_001394319.2:c.56-81A>T (chr16-22166169-A-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001394319.2(SDR42E2):c.56-81A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00671 in 431,390 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0060 ( 7 hom., cov: 32)

Exomes 𝑓: 0.0071 ( 12 hom. )

Consequence

SDR42E2
NM_001394319.2 intron

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.169

Publications

0 publications found

Variant links:

Genes affected

SDR42E2 (HGNC:35414): (short chain dehydrogenase/reductase family 42E, member 2) Predicted to enable oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor. Predicted to be involved in steroid biosynthetic process. [provided by Alliance of Genome Resources, Apr 2022]

SDR42E2 links:

ENSG00000301964 (HGNC:):

ENSG00000301964 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 16-22166169-A-T is Benign according to our data. Variant chr16-22166169-A-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2646310.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394319.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDR42E2	NM_001394319.2	MANE Select	c.56-81A>T		intron	N/A	NP_001381248.1	A6NKP2
	SDR42E2	NM_001365288.2		c.587A>T	p.Glu196Val	missense	Exon 2 of 12	NP_001352217.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SDR42E2	ENST00000602312.3	TSL:5 MANE Select	c.56-81A>T		intron	N/A	ENSP00000473474.2	A6NKP2
SDR42E2	ENST00000686682.1		c.587A>T	p.Glu196Val	missense	Exon 2 of 9	ENSP00000509391.1	A0A8I5KWA0
SDR42E2	ENST00000684942.1		n.587A>T		non_coding_transcript_exon	Exon 2 of 11	ENSP00000508835.1	A0A8I5QKM4

Frequencies

GnomAD3 genomes

AF:

0.00599

AC:

905

AN:

151186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00201

Gnomad AMI

AF:

0.00659

Gnomad AMR

AF:

0.00428

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00804

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00952

Gnomad OTH

AF:

0.00289

GnomAD4 exome

AF:

0.00710

AC:

1989

AN:

280082

Hom.:

AF XY:

0.00720

AC XY:

1046

AN XY:

145348

show subpopulations

African (AFR)

AF:

0.00191

AC:

AN:

7344

American (AMR)

AF:

0.00460

AC:

AN:

7828

Ashkenazi Jewish (ASJ)

AF:

0.00429

AC:

AN:

9796

East Asian (EAS)

AF:

0.00

AC:

AN:

23236

South Asian (SAS)

AF:

0.00110

AC:

AN:

10890

European-Finnish (FIN)

AF:

0.00732

AC:

168

AN:

22966

Middle Eastern (MID)

AF:

0.00247

AC:

AN:

1622

European-Non Finnish (NFE)

AF:

0.00895

AC:

1598

AN:

178540

Other (OTH)

AF:

0.00644

AC:

115

AN:

17860

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

108

216

325

433

541

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.00598

AC:

905

AN:

151308

Hom.:

Cov.:

AF XY:

0.00558

AC XY:

413

AN XY:

73970

show subpopulations

African (AFR)

AF:

0.00200

AC:

AN:

40968

American (AMR)

AF:

0.00428

AC:

AN:

15202

Ashkenazi Jewish (ASJ)

AF:

0.00288

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5138

South Asian (SAS)

AF:

0.00104

AC:

AN:

4792

European-Finnish (FIN)

AF:

0.00804

AC:

AN:

10576

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00952

AC:

646

AN:

67860

Other (OTH)

AF:

0.00286

AC:

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

147

196

245

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:

0.00709

Hom.:

Bravo

AF:

0.00564

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.17

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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