rs1399634

Variant names:

• chr2-169388097-T-A
• rs1399634

Your query was ambiguous. Multiple possible variants found:

• chr2-169388097-T-A
• chr2-169388097-T-C
• chr2-169388097-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;