rs2808628

Variant names:

• chr1-159706221-G-A
• rs2808628

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 0.316 in 152,040 control chromosomes in the GnomAD database, including 8,111 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 0.32 (8111 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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: 0.316 AC: 47994 AN: 151922 Hom.: 8103 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.316 AC: 48018 AN: 152040 Hom.: 8111 Cov.: 32 AF XY: 0.320 AC XY: 23788 AN XY: 74296

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.333

Alfa AF: 0.327 Hom.: 7721

Bravo AF: 0.311

Asia WGS AF: 0.440 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2808628; hg19: chr1-159676011;