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. Variant got -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

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 (AFR) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.893

Gnomad4 AMR AF: 0.855

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.896

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.845

Alfa AF: 0.842 Hom.: 117348

Bravo AF: 0.858

Asia WGS AF: 0.781 AC: 2716 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	0.85
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4713858; hg19: chr6-35402785;