rs2808630

Variant names:

• chr1-159711078-C-T
• rs2808630

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 0.768 in 152,164 control chromosomes in the GnomAD database, including 45,128 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 0.77 (45128 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 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: 0.768 AC: 116795 AN: 152046 Hom.: 45080 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.768 AC: 116903 AN: 152164 Hom.: 45128 Cov.: 32 AF XY: 0.770 AC XY: 57307 AN XY: 74390

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.775

Alfa AF: 0.729 Hom.: 87398

Bravo AF: 0.773

Asia WGS AF: 0.741 AC: 2578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2808630; hg19: chr1-159680868;