rs1447352

chr11-92989595-G-Achr11-92989595-G-Cchr11-92989595-G-T

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 0.557 in 151,970 control chromosomes in the GnomAD database, including 23,909 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 0.56 (23909 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 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: 0.557 AC: 84529 AN: 151852 Hom.: 23876 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.557 AC: 84625 AN: 151970 Hom.: 23909 Cov.: 32 AF XY: 0.565 AC XY: 41959 AN XY: 74254

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.541

Alfa AF: 0.529 Hom.: 32614

Bravo AF: 0.564

Asia WGS AF: 0.650 AC: 2259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.0
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1447352; hg19: chr11-92722761; COSMIC: COSV73276624;