rs35265698

Positions:

• chr6-32593557-C-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 0.132 in 151,862 control chromosomes in the GnomAD database, including 1,686 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 0.13 (1686 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.206 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: 0.132 AC: 20016 AN: 151744 Hom.: 1685 Cov.: 31

Gnomad AFR AF: 0.0489

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.132 AC: 20041 AN: 151862 Hom.: 1686 Cov.: 31 AF XY: 0.132 AC XY: 9772 AN XY: 74236

Gnomad4 AFR AF: 0.0491

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0772

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.120

Alfa AF: 0.152 Hom.: 226

Bravo AF: 0.140

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
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: rs35265698; hg19: chr6-32561334;