rs1399634

chr2-169388097-T-Achr2-169388097-T-Cchr2-169388097-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.687

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	15
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1399634; hg19: chr2-170244607;