rs7112005

Variant names:

• chr11-13217953-T-C
• rs7112005

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 0.745 in 152,062 control chromosomes in the GnomAD database, including 42,518 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 0.75 (42518 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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: 0.745 AC: 113268 AN: 151944 Hom.: 42501 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.745 AC: 113329 AN: 152062 Hom.: 42518 Cov.: 32 AF XY: 0.742 AC XY: 55170 AN XY: 74344

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.754

Alfa AF: 0.777 Hom.: 93027

Bravo AF: 0.740

Asia WGS AF: 0.778 AC: 2706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7112005; hg19: chr11-13239500;