rs686708

Variant names:

• chr6-116770520-T-C
• rs686708

Your query was ambiguous. Multiple possible variants found:

• chr6-116770520-T-C
• chr6-116770520-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.730 AC: 30253 AN: 41416

American (AMR) AF: 0.614 AC: 9379 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2284 AN: 3468

East Asian (EAS) AF: 0.513 AC: 2639 AN: 5142

South Asian (SAS) AF: 0.454 AC: 2187 AN: 4820

European-Finnish (FIN) AF: 0.435 AC: 4598 AN: 10560

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31636 AN: 67956

Other (OTH) AF: 0.582 AC: 1229 AN: 2112

Alfa AF: 0.523 Hom.: 45436

Bravo AF: 0.582

Asia WGS AF: 0.510 AC: 1774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.6
DANN	Benign	0.73
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs686708; hg19: chr6-117091683;