rs6677719

Variant names:

• chr1-159753330-C-T
• rs6677719

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 0.767 in 152,186 control chromosomes in the GnomAD database, including 45,868 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 (45868 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.987

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 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: 0.767 AC: 116625 AN: 152068 Hom.: 45808 Cov.: 32

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.767 AC: 116742 AN: 152186 Hom.: 45868 Cov.: 32 AF XY: 0.766 AC XY: 57015 AN XY: 74404

Gnomad4 AFR AF: 0.942

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.763

Alfa AF: 0.724 Hom.: 5025

Bravo AF: 0.786

Asia WGS AF: 0.754 AC: 2624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6677719; hg19: chr1-159723120;