rs7124781

Variant names:

• chr11-42535248-A-C
• rs7124781

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 0.495 in 151,904 control chromosomes in the GnomAD database, including 18,946 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 (18946 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.564 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: 0.495 AC: 75175 AN: 151786 Hom.: 18933 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.495 AC: 75228 AN: 151904 Hom.: 18946 Cov.: 32 AF XY: 0.496 AC XY: 36855 AN XY: 74234

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.514

Alfa AF: 0.514 Hom.: 2513

Bravo AF: 0.485

Asia WGS AF: 0.444 AC: 1545 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7124781; hg19: chr11-42556798;