rs6685280

Variant names:

• chr1-186716686-C-A
• rs6685280

Your query was ambiguous. Multiple possible variants found:

• chr1-186716686-C-A
• chr1-186716686-C-G
• chr1-186716686-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 0.747 in 152,140 control chromosomes in the GnomAD database, including 43,018 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 0.75 (43018 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

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 (EAS) allele frequency at 95% confidence interval = 0.927 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: 0.747 AC: 113617 AN: 152022 Hom.: 43010 Cov.: 33

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.747 AC: 113650 AN: 152140 Hom.: 43018 Cov.: 33 AF XY: 0.753 AC XY: 55979 AN XY: 74382

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.742

Alfa AF: 0.769 Hom.: 71628

Bravo AF: 0.741

Asia WGS AF: 0.793 AC: 2757 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	0.22
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6685280; hg19: chr1-186685818; COSMIC: COSV59997195;