dbSNP rs621942: ENSG00000309910:n.*195C>A (chr11-86072696-C-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000845444.1(ENSG00000309910):n.*195C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,874 control chromosomes in the GnomAD database, including 5,425 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 0.26 ( 5425 hom., cov: 32)

Consequence

ENSG00000309910
ENST00000845444.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.264

Publications

11 publications found

Variant links:

Genes affected

ENSG00000309910 (HGNC:):

ENSG00000309910 links:

Genome browser will be placed here

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=-0.44).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902731	XR_007062823.1 link	n.*195C>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309910	ENST00000845444.1 link	n.*195C>A		downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39550

AN:

151754

Hom.:

5425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.331

Gnomad AMI

AF:

0.367

Gnomad AMR

AF:

0.271

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.112

Gnomad SAS

AF:

0.281

Gnomad FIN

AF:

0.149

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.258

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.261

AC:

39572

AN:

151874

Hom.:

5425

Cov.:

AF XY:

0.258

AC XY:

19117

AN XY:

74226

show subpopulations

African (AFR)

AF:

0.331

AC:

13694

AN:

41392

American (AMR)

AF:

0.271

AC:

4131

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

865

AN:

3462

East Asian (EAS)

AF:

0.112

AC:

580

AN:

5166

South Asian (SAS)

AF:

0.282

AC:

1355

AN:

4810

European-Finnish (FIN)

AF:

0.149

AC:

1574

AN:

10534

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.242

AC:

16417

AN:

67932

Other (OTH)

AF:

0.257

AC:

542

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1462

2925

4387

5850

7312

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

412

824

1236

1648

2060

<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:

0.247

Hom.:

19701

Bravo

AF:

0.270

Asia WGS

AF:

0.182

AC:

637

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

(source)

DANN

Benign

0.75

PhyloP100

0.26

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over