dbSNP rs12534221: ENSG00000306749:n.457-12175C>A (chr7-131603231-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000820764.1(ENSG00000306749):n.457-12175C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,136 control chromosomes in the GnomAD database, including 1,694 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 0.13 ( 1694 hom., cov: 32)

Consequence

ENSG00000306749
ENST00000820764.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.783

Publications

12 publications found

Variant links:

Genes affected

ENSG00000306749 (HGNC:):

ENSG00000306749 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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 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
ENSG00000306749	ENST00000820764.1 link	n.457-12175C>A		intron_variant	Intron 3 of 3
ENSG00000306749	ENST00000820765.1 link	n.435-12175C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20375

AN:

152018

Hom.:

1697

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0509

Gnomad AMI

AF:

0.0471

Gnomad AMR

AF:

0.161

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.295

Gnomad SAS

AF:

0.162

Gnomad FIN

AF:

0.206

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.153

Gnomad OTH

AF:

0.150

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

GnomAD4 genome

AF:

0.134

AC:

20372

AN:

152136

Hom.:

1694

Cov.:

AF XY:

0.137

AC XY:

10223

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.0508

AC:

2109

AN:

41534

American (AMR)

AF:

0.161

AC:

2461

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.159

AC:

552

AN:

3472

East Asian (EAS)

AF:

0.294

AC:

1512

AN:

5136

South Asian (SAS)

AF:

0.162

AC:

781

AN:

4814

European-Finnish (FIN)

AF:

0.206

AC:

2182

AN:

10570

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.153

AC:

10384

AN:

68004

Other (OTH)

AF:

0.149

AC:

315

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

919

1838

2758

3677

4596

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

234

468

702

936

1170

<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:

0.149

Hom.:

6176

Bravo

AF:

0.129

Asia WGS

AF:

0.214

AC:

740

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.0

(source)

DANN

Benign

0.58

PhyloP100

0.78

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