rs6686886

chr1-156386688-G-Achr1-156386688-G-Cchr1-156386688-G-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 0.818 in 152,220 control chromosomes in the GnomAD database, including 51,287 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 0.82 (51287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124405 AN: 152102 Hom.: 51244 Cov.: 32

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.818 AC: 124511 AN: 152220 Hom.: 51287 Cov.: 32 AF XY: 0.814 AC XY: 60553 AN XY: 74410

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.879

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.786

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.823

Alfa AF: 0.845 Hom.: 88379

Bravo AF: 0.816

Asia WGS AF: 0.731 AC: 2545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.2
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6686886; hg19: chr1-156356480;