rs11752643

Positions:

• chr6-32701596-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0233 in 144,972 control chromosomes in the GnomAD database, including 47 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 0.023 (47 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0233 (3381/144972) while in subpopulation NFE AF= 0.0327 (2171/66446). AF 95% confidence interval is 0.0315. There are 47 homozygotes in gnomad4. There are 1643 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 47 gene

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: 0.0233 AC: 3377 AN: 144868 Hom.: 47 Cov.: 31

Gnomad AFR AF: 0.00943

Gnomad AMI AF: 0.0413

Gnomad AMR AF: 0.0138

Gnomad ASJ AF: 0.0125

Gnomad EAS AF: 0.0149

Gnomad SAS AF: 0.0125

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.00974

Gnomad NFE AF: 0.0327

Gnomad OTH AF: 0.0223

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

GnomAD4 genome AF: 0.0233 AC: 3381 AN: 144972 Hom.: 47 Cov.: 31 AF XY: 0.0233 AC XY: 1643 AN XY: 70546

Gnomad4 AFR AF: 0.00948

Gnomad4 AMR AF: 0.0138

Gnomad4 ASJ AF: 0.0125

Gnomad4 EAS AF: 0.0150

Gnomad4 SAS AF: 0.0127

Gnomad4 FIN AF: 0.0416

Gnomad4 NFE AF: 0.0327

Gnomad4 OTH AF: 0.0220

Alfa AF: 0.0291 Hom.: 97

Bravo AF: 0.0210

Asia WGS AF: 0.0150 AC: 50 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11752643; hg19: chr6-32669373;