rs11072512

Variant names:

• chr15-74911685-C-T
• rs11072512

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 0.374 in 151,996 control chromosomes in the GnomAD database, including 13,509 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 0.37 (13509 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.535 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: 0.375 AC: 56893 AN: 151878 Hom.: 13509 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.374 AC: 56898 AN: 151996 Hom.: 13509 Cov.: 32 AF XY: 0.365 AC XY: 27108 AN XY: 74276

African (AFR) AF: 0.104 AC: 4328 AN: 41464

American (AMR) AF: 0.436 AC: 6653 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1604 AN: 3472

East Asian (EAS) AF: 0.180 AC: 931 AN: 5178

South Asian (SAS) AF: 0.181 AC: 870 AN: 4812

European-Finnish (FIN) AF: 0.430 AC: 4533 AN: 10534

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36639 AN: 67956

Other (OTH) AF: 0.391 AC: 825 AN: 2112

Alfa AF: 0.482 Hom.: 23846

Bravo AF: 0.370

Asia WGS AF: 0.173 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.70
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs11072512; hg19: chr15-75204026;