rs677618

Variant names:

• chr1-181857976-C-T
• rs677618

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 0.762 in 152,068 control chromosomes in the GnomAD database, including 44,751 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 0.76 (44751 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 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: 0.762 AC: 115852 AN: 151950 Hom.: 44706 Cov.: 31

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.762 AC: 115946 AN: 152068 Hom.: 44751 Cov.: 31 AF XY: 0.760 AC XY: 56506 AN XY: 74318

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.758

Alfa AF: 0.720 Hom.: 54245

Bravo AF: 0.768

Asia WGS AF: 0.701 AC: 2438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs677618; hg19: chr1-181827111;