chr2-169388097-T-A

Variant names:

• chr2-169388097-T-A
• rs1399634

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 0.68 in 152,004 control chromosomes in the GnomAD database, including 37,345 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 (37345 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103293 AN: 151886 Hom.: 37320 Cov.: 31

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.680 AC: 103340 AN: 152004 Hom.: 37345 Cov.: 31 AF XY: 0.683 AC XY: 50725 AN XY: 74292

African (AFR) AF: 0.434 AC: 17953 AN: 41394

American (AMR) AF: 0.753 AC: 11504 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2468 AN: 3470

East Asian (EAS) AF: 0.402 AC: 2072 AN: 5160

South Asian (SAS) AF: 0.725 AC: 3491 AN: 4816

European-Finnish (FIN) AF: 0.836 AC: 8842 AN: 10576

Middle Eastern (MID) AF: 0.736 AC: 215 AN: 292

European-Non Finnish (NFE) AF: 0.802 AC: 54499 AN: 67990

Other (OTH) AF: 0.687 AC: 1450 AN: 2112

Alfa AF: 0.732 Hom.: 5251

Bravo AF: 0.658

Asia WGS AF: 0.571 AC: 1988 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	15
DANN	Benign	0.85
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1399634; hg19: chr2-170244607; COSMIC: COSV107166072;