rs1502242

Variant names:

• chr11-13604072-C-A
• rs1502242

Your query was ambiguous. Multiple possible variants found:

• chr11-13604072-C-A
• chr11-13604072-C-G
• chr11-13604072-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0796 AC: 3308 AN: 41550

American (AMR) AF: 0.207 AC: 3164 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3472

East Asian (EAS) AF: 0.340 AC: 1760 AN: 5176

South Asian (SAS) AF: 0.132 AC: 637 AN: 4820

European-Finnish (FIN) AF: 0.0766 AC: 810 AN: 10580

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7588 AN: 67978

Other (OTH) AF: 0.125 AC: 264 AN: 2110

Alfa AF: 0.110 Hom.: 829

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
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs1502242; hg19: chr11-13625619;