6-35435008-A-G

Position:

• chr6-35435008-A-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 0.859 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;