rs2808630

chr1-159711078-C-T

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/exons	MANE	UniProt

Ensembl

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