rs2732546

Positions:

• chr11-35067538-T-C
• chr11-35067538-T-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 0.496 in 151,920 control chromosomes in the GnomAD database, including 20,153 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 0.50 (20153 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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: 0.496 AC: 75272 AN: 151802 Hom.: 20150 Cov.: 31

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.496 AC: 75279 AN: 151920 Hom.: 20153 Cov.: 31 AF XY: 0.501 AC XY: 37225 AN XY: 74258

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.538

Alfa AF: 0.396 Hom.: 1184

Bravo AF: 0.490

Asia WGS AF: 0.685 AC: 2381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2732546; hg19: chr11-35089085;