dbSNP rs12189640: ENSG00000285703:n.107-10779A>G (chr6-27506878-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The ENST00000648816.1(ENSG00000285703):n.107-10779A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0488 in 152,278 control chromosomes in the GnomAD database, including 264 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 0.049 ( 264 hom., cov: 32)

Consequence

ENSG00000285703
ENST00000648816.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.45

Publications

2 publications found

Variant links:

Genes affected

ENSG00000285703 (HGNC:):

ENSG00000285703 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=-0.29).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000285703	ENST00000648816.1 link	n.107-10779A>G	intron_variant	Intron 1 of 3
ENSG00000286652	ENST00000779964.1 link	n.280-6518T>C	intron_variant	Intron 2 of 3
ENSG00000286652	ENST00000779965.1 link	n.276-8089T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0488

AC:

7432

AN:

152162

Hom.:

264

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0124

Gnomad AMI

AF:

0.0879

Gnomad AMR

AF:

0.0328

Gnomad ASJ

AF:

0.0222

Gnomad EAS

AF:

0.00289

Gnomad SAS

AF:

0.0212

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0730

Gnomad OTH

AF:

0.0349

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

GnomAD4 genome

AF:

0.0488

AC:

7432

AN:

152278

Hom.:

264

Cov.:

AF XY:

0.0492

AC XY:

3661

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.0124

AC:

514

AN:

41564

American (AMR)

AF:

0.0328

AC:

502

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0222

AC:

AN:

3466

East Asian (EAS)

AF:

0.00289

AC:

AN:

5184

South Asian (SAS)

AF:

0.0214

AC:

103

AN:

4818

European-Finnish (FIN)

AF:

0.103

AC:

1097

AN:

10618

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0730

AC:

4968

AN:

68022

Other (OTH)

AF:

0.0345

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

354

708

1062

1416

1770

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

270

360

450

<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:

0.0611

Hom.:

648

Bravo

AF:

0.0430

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

1.5

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