1-186716686-C-A

Position:

• chr1-186716686-C-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;