dbSNP rs2734986: ENSG00000290870:n.2321-162A>G (chr6-29850791-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 ENST00000647952.1(ENSG00000290870):n.2321-162A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,172 control chromosomes in the GnomAD database, including 1,109 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 0.10 ( 1109 hom., cov: 31)

Consequence

ENSG00000290870
ENST00000647952.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.819

Publications

30 publications found

Variant links:

Genes affected

ENSG00000290870 (HGNC:):

ENSG00000290870 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105375010	XR_926680.3 link	n.207-162A>G	intron_variant	Intron 2 of 2
LOC105375010	XR_926681.2 link	n.207-162A>G	intron_variant	Intron 2 of 3
LOC105375010	XR_926682.3 link	n.206+1531A>G	intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290870	ENST00000647952.1 link	n.2321-162A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15780

AN:

152054

Hom.:

1109

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0335

Gnomad AMI

AF:

0.172

Gnomad AMR

AF:

0.0675

Gnomad ASJ

AF:

0.121

Gnomad EAS

AF:

0.0183

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.0780

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.162

Gnomad OTH

AF:

0.0982

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

GnomAD4 genome

AF:

0.104

AC:

15773

AN:

152172

Hom.:

1109

Cov.:

AF XY:

0.0987

AC XY:

7345

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.0335

AC:

1390

AN:

41550

American (AMR)

AF:

0.0674

AC:

1029

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.121

AC:

418

AN:

3468

East Asian (EAS)

AF:

0.0184

AC:

AN:

5170

South Asian (SAS)

AF:

0.128

AC:

619

AN:

4824

European-Finnish (FIN)

AF:

0.0780

AC:

825

AN:

10574

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.162

AC:

10997

AN:

67996

Other (OTH)

AF:

0.0976

AC:

206

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

700

1400

2099

2799

3499

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

198

396

594

792

990

<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:

0.140

Hom.:

2940

Bravo

AF:

0.0983

Asia WGS

AF:

0.0630

AC:

221

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

6.3

(source)

DANN

Benign

0.48

PhyloP100

-0.82

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