rs35265698

Variant names:

• chr6-32593557-C-G
• rs35265698

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 0.132 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
• Publications: 27 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0491 AC: 2036 AN: 41468

American (AMR) AF: 0.212 AC: 3233 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3468

East Asian (EAS) AF: 0.153 AC: 791 AN: 5170

South Asian (SAS) AF: 0.0772 AC: 372 AN: 4816

European-Finnish (FIN) AF: 0.142 AC: 1492 AN: 10528

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10953 AN: 67880

Other (OTH) AF: 0.120 AC: 251 AN: 2094

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs35265698; hg19: chr6-32561334;