rs11752643

Variant names:

• chr6-32701596-C-T
• rs11752643

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 33 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 47 gene

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: 0.0233 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

African (AFR) AF: 0.00948 AC: 367 AN: 38704

American (AMR) AF: 0.0138 AC: 198 AN: 14328

Ashkenazi Jewish (ASJ) AF: 0.0125 AC: 42 AN: 3368

East Asian (EAS) AF: 0.0150 AC: 75 AN: 5012

South Asian (SAS) AF: 0.0127 AC: 60 AN: 4714

European-Finnish (FIN) AF: 0.0416 AC: 386 AN: 9270

Middle Eastern (MID) AF: 0.0105 AC: 3 AN: 286

European-Non Finnish (NFE) AF: 0.0327 AC: 2171 AN: 66446

Other (OTH) AF: 0.0220 AC: 44 AN: 1996

Alfa AF: 0.0286 Hom.: 268

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
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs11752643; hg19: chr6-32669373;