rs2808629

Variant names:

• chr1-159707006-G-A
• rs2808629

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 0.312 in 151,864 control chromosomes in the GnomAD database, including 7,980 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 0.31 (7980 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 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: 0.312 AC: 47353 AN: 151746 Hom.: 7973 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.312 AC: 47379 AN: 151864 Hom.: 7980 Cov.: 32 AF XY: 0.317 AC XY: 23515 AN XY: 74212

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.330

Alfa AF: 0.315 Hom.: 2189

Bravo AF: 0.306

Asia WGS AF: 0.440 AC: 1527 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2808629; hg19: chr1-159676796;