rs7112005

Variant names:

• chr11-13217953-T-C
• rs7112005

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 0.745 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.698 AC: 28948 AN: 41458

American (AMR) AF: 0.703 AC: 10742 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2575 AN: 3468

East Asian (EAS) AF: 0.822 AC: 4257 AN: 5178

South Asian (SAS) AF: 0.777 AC: 3752 AN: 4830

European-Finnish (FIN) AF: 0.697 AC: 7359 AN: 10554

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53231 AN: 67984

Other (OTH) AF: 0.754 AC: 1590 AN: 2108

Alfa AF: 0.771 Hom.: 141375

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs7112005; hg19: chr11-13239500;