dbSNP rs12629805: ENSG00000243620:n.544-4666A>G (chr3-146914377-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000473299.1(ENSG00000243620):n.544-4666A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,156 control chromosomes in the GnomAD database, including 1,170 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 0.12 ( 1170 hom., cov: 32)

Consequence

ENSG00000243620
ENST00000473299.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.617

Publications

6 publications found

Variant links:

Genes affected

ENSG00000243620 (HGNC:):

ENSG00000243620 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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
ENSG00000243620	ENST00000473299.1 link	n.544-4666A>G		intron_variant	Intron 5 of 5	4
ENSG00000243620	ENST00000776315.1 link	n.384-4666A>G		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes

AF:

0.117

AC:

17814

AN:

152038

Hom.:

1171

Cov.:

show subpopulations

Gnomad AFR

AF:

0.179

Gnomad AMI

AF:

0.0296

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.0905

Gnomad EAS

AF:

0.0410

Gnomad SAS

AF:

0.0659

Gnomad FIN

AF:

0.0861

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.100

Gnomad OTH

AF:

0.120

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

GnomAD4 genome

AF:

0.117

AC:

17840

AN:

152156

Hom.:

1170

Cov.:

AF XY:

0.114

AC XY:

8466

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.178

AC:

7407

AN:

41508

American (AMR)

AF:

0.101

AC:

1546

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0905

AC:

314

AN:

3470

East Asian (EAS)

AF:

0.0413

AC:

214

AN:

5180

South Asian (SAS)

AF:

0.0663

AC:

320

AN:

4824

European-Finnish (FIN)

AF:

0.0861

AC:

913

AN:

10606

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.100

AC:

6802

AN:

67972

Other (OTH)

AF:

0.123

AC:

261

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

798

1596

2394

3192

3990

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.112

Hom.:

127

Bravo

AF:

0.123

Asia WGS

AF:

0.0850

AC:

296

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.3

(source)

DANN

Benign

0.68

PhyloP100

-0.62

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