rs1502242

chr11-13604072-C-Achr11-13604072-C-Gchr11-13604072-C-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 0.121 in 152,176 control chromosomes in the GnomAD database, including 1,463 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 0.12 (1463 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.543

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 = 0.327 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: 0.121 AC: 18348 AN: 152058 Hom.: 1463 Cov.: 32

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0766

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.121 AC: 18354 AN: 152176 Hom.: 1463 Cov.: 32 AF XY: 0.123 AC XY: 9153 AN XY: 74404

Gnomad4 AFR AF: 0.0796

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0766

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.125

Alfa AF: 0.108 Hom.: 660

Bravo AF: 0.128

Asia WGS AF: 0.208 AC: 724 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	14
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1502242; hg19: chr11-13625619;