dbSNP rs9965495: ENSG00000285681:n.113+37098G>A (chr18-60366443-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 ENST00000650201.1(ENSG00000285681):n.113+37098G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,966 control chromosomes in the GnomAD database, including 10,920 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 0.36 ( 10920 hom., cov: 32)

Consequence

ENSG00000285681
ENST00000650201.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0820

Publications

8 publications found

Variant links:

Genes affected

ENSG00000285681 (HGNC:):

ENSG00000285681 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 (BayesDel_noAF=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285681	ENST00000650201.1 link	n.113+37098G>A		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1 link	n.156+37098G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54641

AN:

151848

Hom.:

10904

Cov.:

show subpopulations

Gnomad AFR

AF:

0.531

Gnomad AMI

AF:

0.368

Gnomad AMR

AF:

0.309

Gnomad ASJ

AF:

0.271

Gnomad EAS

AF:

0.131

Gnomad SAS

AF:

0.284

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.310

Gnomad OTH

AF:

0.343

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

GnomAD4 genome

AF:

0.360

AC:

54692

AN:

151966

Hom.:

10920

Cov.:

AF XY:

0.351

AC XY:

26092

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.532

AC:

22036

AN:

41446

American (AMR)

AF:

0.308

AC:

4704

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.271

AC:

940

AN:

3470

East Asian (EAS)

AF:

0.131

AC:

679

AN:

5178

South Asian (SAS)

AF:

0.283

AC:

1363

AN:

4822

European-Finnish (FIN)

AF:

0.264

AC:

2781

AN:

10542

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.310

AC:

21053

AN:

67912

Other (OTH)

AF:

0.340

AC:

719

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1691

3382

5074

6765

8456

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

522

1044

1566

2088

2610

<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:

0.340

Hom.:

1186

Bravo

AF:

0.375

Asia WGS

AF:

0.230

AC:

801

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.50

(source)

DANN

Benign

0.21

PhyloP100

0.082

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