rs4713858

Variant names:

• chr6-35435008-A-G
• rs4713858

Your query was ambiguous. Multiple possible variants found:

• chr6-35435008-A-G
• chr6-35435008-A-T

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 0.859 in 151,770 control chromosomes in the GnomAD database, including 56,153 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 0.86 (56153 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 45 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.885 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: 0.859 AC: 130294 AN: 151654 Hom.: 56101 Cov.: 28

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.859 AC: 130404 AN: 151770 Hom.: 56153 Cov.: 28 AF XY: 0.860 AC XY: 63780 AN XY: 74202

African (AFR) AF: 0.893 AC: 36941 AN: 41362

American (AMR) AF: 0.855 AC: 13015 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2646 AN: 3468

East Asian (EAS) AF: 0.744 AC: 3829 AN: 5146

South Asian (SAS) AF: 0.855 AC: 4097 AN: 4792

European-Finnish (FIN) AF: 0.896 AC: 9430 AN: 10522

Middle Eastern (MID) AF: 0.863 AC: 252 AN: 292

European-Non Finnish (NFE) AF: 0.848 AC: 57617 AN: 67950

Other (OTH) AF: 0.845 AC: 1779 AN: 2106

Alfa AF: 0.848 Hom.: 246336

Bravo AF: 0.858

Asia WGS AF: 0.781 AC: 2716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.85
DANN	Benign	0.43
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs4713858; hg19: chr6-35402785;