rs686708

chr6-116770520-T-Cchr6-116770520-T-G

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 0.559 in 151,954 control chromosomes in the GnomAD database, including 24,876 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 0.56 (24876 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 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: 0.559 AC: 84832 AN: 151836 Hom.: 24837 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.559 AC: 84931 AN: 151954 Hom.: 24876 Cov.: 32 AF XY: 0.556 AC XY: 41302 AN XY: 74250

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.582

Alfa AF: 0.503 Hom.: 24937

Bravo AF: 0.582

Asia WGS AF: 0.510 AC: 1774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	4.6
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs686708; hg19: chr6-117091683;