dbSNP rs1486860: ENSG00000309690:n.34-23603A>G (chr4-112472287-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 ENST00000843046.1(ENSG00000309690):n.34-23603A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,006 control chromosomes in the GnomAD database, including 11,967 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 0.39 ( 11967 hom., cov: 32)

Consequence

ENSG00000309690
ENST00000843046.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.871

Publications

4 publications found

Variant links:

Genes affected

ENSG00000309690 (HGNC:):

ENSG00000309690 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=-1.01).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.469 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
ENSG00000309690	ENST00000843046.1 link	n.34-23603A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.394

AC:

59890

AN:

151888

Hom.:

11961

Cov.:

show subpopulations

Gnomad AFR

AF:

0.397

Gnomad AMI

AF:

0.287

Gnomad AMR

AF:

0.477

Gnomad ASJ

AF:

0.313

Gnomad EAS

AF:

0.334

Gnomad SAS

AF:

0.446

Gnomad FIN

AF:

0.378

Gnomad MID

AF:

0.418

Gnomad NFE

AF:

0.383

Gnomad OTH

AF:

0.383

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

GnomAD4 genome

AF:

0.394

AC:

59926

AN:

152006

Hom.:

11967

Cov.:

AF XY:

0.395

AC XY:

29357

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.396

AC:

16428

AN:

41460

American (AMR)

AF:

0.478

AC:

7295

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.313

AC:

1086

AN:

3468

East Asian (EAS)

AF:

0.334

AC:

1731

AN:

5176

South Asian (SAS)

AF:

0.448

AC:

2157

AN:

4816

European-Finnish (FIN)

AF:

0.378

AC:

3985

AN:

10550

Middle Eastern (MID)

AF:

0.415

AC:

122

AN:

294

European-Non Finnish (NFE)

AF:

0.383

AC:

26054

AN:

67960

Other (OTH)

AF:

0.382

AC:

807

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1858

3715

5573

7430

9288

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

574

1148

1722

2296

2870

<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:

0.389

Hom.:

19271

Bravo

AF:

0.402

Asia WGS

AF:

0.453

AC:

1572

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

5.8

(source)

DANN

Benign

0.43

PhyloP100

-0.87

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