rs6679677

Variant names:

• chr1-113761186-C-A
• rs6679677

Your query was ambiguous. Multiple possible variants found:

• chr1-113761186-C-A
• chr1-113761186-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 0.0655 in 152,258 control chromosomes in the GnomAD database, including 484 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 0.066 (484 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0984 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: 0.0656 AC: 9974 AN: 152140 Hom.: 484 Cov.: 32

Gnomad AFR AF: 0.0152

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0380

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0655 AC: 9974 AN: 152258 Hom.: 484 Cov.: 32 AF XY: 0.0644 AC XY: 4795 AN XY: 74438

Gnomad4 AFR AF: 0.0151

Gnomad4 AMR AF: 0.0380

Gnomad4 ASJ AF: 0.0501

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0124

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.0853 Hom.: 941

Bravo AF: 0.0555

Asia WGS AF: 0.00866 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6679677; hg19: chr1-114303808;