chr2-15821475-G-C

Variant names:

• chr2-15821475-G-C
• rs7586898

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.679 in 152,132 control chromosomes in the GnomAD database, including 38,079 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 0.68 (38079 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103211 AN: 152014 Hom.: 38070 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.679 AC: 103251 AN: 152132 Hom.: 38079 Cov.: 33 AF XY: 0.680 AC XY: 50592 AN XY: 74358

African (AFR) AF: 0.379 AC: 15710 AN: 41500

American (AMR) AF: 0.687 AC: 10500 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2928 AN: 3470

East Asian (EAS) AF: 0.530 AC: 2727 AN: 5146

South Asian (SAS) AF: 0.729 AC: 3514 AN: 4820

European-Finnish (FIN) AF: 0.829 AC: 8779 AN: 10586

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56627 AN: 68010

Other (OTH) AF: 0.707 AC: 1494 AN: 2112

Alfa AF: 0.683 Hom.: 2422

Bravo AF: 0.653

Asia WGS AF: 0.599 AC: 2084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.0
DANN	Benign	0.65
PhyloP100		-0.060

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7586898; hg19: chr2-15961599;