rs2732544

chr11-35071404-T-C

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 0.595 in 151,964 control chromosomes in the GnomAD database, including 27,148 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 0.59 (27148 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90263 AN: 151846 Hom.: 27111 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.595 AC: 90345 AN: 151964 Hom.: 27148 Cov.: 32 AF XY: 0.600 AC XY: 44545 AN XY: 74276

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.791

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.622

Alfa AF: 0.572 Hom.: 3125

Bravo AF: 0.598

Asia WGS AF: 0.761 AC: 2647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.31
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2732544; hg19: chr11-35092951;