2-163239954-A-G

Variant names:

• chr2-163239954-A-G
• rs1587805

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 0.927 in 152,172 control chromosomes in the GnomAD database, including 65,840 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 0.93 (65840 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.973 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: 0.928 AC: 141033 AN: 152054 Hom.: 65820 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.973

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.935

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

GnomAD4 genome AF: 0.927 AC: 141101 AN: 152172 Hom.: 65840 Cov.: 31 AF XY: 0.926 AC XY: 68868 AN XY: 74390

African (AFR) AF: 0.822 AC: 34115 AN: 41484

American (AMR) AF: 0.960 AC: 14675 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.973 AC: 3376 AN: 3470

East Asian (EAS) AF: 0.804 AC: 4148 AN: 5156

South Asian (SAS) AF: 0.932 AC: 4500 AN: 4828

European-Finnish (FIN) AF: 0.992 AC: 10527 AN: 10612

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.979 AC: 66600 AN: 68008

Other (OTH) AF: 0.933 AC: 1974 AN: 2116

Alfa AF: 0.966 Hom.: 39674

Bravo AF: 0.919

Asia WGS AF: 0.873 AC: 3038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.85
DANN	Benign	0.56
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1587805; hg19: chr2-164096464;