rs11172782

chr12-58865846-A-G

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 0.115 in 151,364 control chromosomes in the GnomAD database, including 2,238 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 0.11 (2238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17363 AN: 151250 Hom.: 2234 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0266

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0736

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0152

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.115 AC: 17394 AN: 151364 Hom.: 2238 Cov.: 32 AF XY: 0.113 AC XY: 8356 AN XY: 74010

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0266

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.0732

Gnomad4 FIN AF: 0.0271

Gnomad4 NFE AF: 0.0152

Gnomad4 OTH AF: 0.0958

Alfa AF: 0.0317 Hom.: 359

Bravo AF: 0.130

Asia WGS AF: 0.129 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.1
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11172782; hg19: chr12-59259628;