dbSNP rs10457526: ENSG00000226149:n.48+20C>A (chr6-129575356-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000657779.1(ENSG00000226149):n.48+20C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,992 control chromosomes in the GnomAD database, including 3,960 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 0.22 ( 3960 hom., cov: 31)

Consequence

ENSG00000226149
ENST00000657779.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01

Publications

9 publications found

Variant links:

Genes affected

ENSG00000226149 (HGNC:):

ENSG00000226149 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=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000226149	ENST00000657779.1 link	n.48+20C>A	intron_variant	Intron 1 of 9
ENSG00000226149	ENST00000665046.1 link	n.30+662C>A	intron_variant	Intron 1 of 9
ENSG00000226149	ENST00000670413.1 link	n.48+20C>A	intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33551

AN:

151874

Hom.:

3954

Cov.:

show subpopulations

Gnomad AFR

AF:

0.200

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.334

Gnomad ASJ

AF:

0.190

Gnomad EAS

AF:

0.262

Gnomad SAS

AF:

0.307

Gnomad FIN

AF:

0.215

Gnomad MID

AF:

0.140

Gnomad NFE

AF:

0.204

Gnomad OTH

AF:

0.205

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

GnomAD4 genome

AF:

0.221

AC:

33568

AN:

151992

Hom.:

3960

Cov.:

AF XY:

0.226

AC XY:

16788

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.200

AC:

8282

AN:

41470

American (AMR)

AF:

0.334

AC:

5102

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.190

AC:

660

AN:

3466

East Asian (EAS)

AF:

0.262

AC:

1353

AN:

5162

South Asian (SAS)

AF:

0.305

AC:

1473

AN:

4824

European-Finnish (FIN)

AF:

0.215

AC:

2269

AN:

10538

Middle Eastern (MID)

AF:

0.144

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.204

AC:

13851

AN:

67954

Other (OTH)

AF:

0.203

AC:

429

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1297

2595

3892

5190

6487

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

358

716

1074

1432

1790

<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:

0.211

Hom.:

15628

Bravo

AF:

0.226

Asia WGS

AF:

0.267

AC:

931

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.7

(source)

DANN

Benign

0.59

PhyloP100

1.0

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