rs11616188

Variant names:

• chr12-6393576-G-A
• rs11616188

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 0.298 in 152,166 control chromosomes in the GnomAD database, including 8,638 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 0.30 (8638 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 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: 0.298 AC: 45340 AN: 152048 Hom.: 8641 Cov.: 32

Gnomad AFR AF: 0.0884

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.298 AC: 45338 AN: 152166 Hom.: 8638 Cov.: 32 AF XY: 0.299 AC XY: 22208 AN XY: 74362

African (AFR) AF: 0.0882 AC: 3664 AN: 41544

American (AMR) AF: 0.263 AC: 4019 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1060 AN: 3472

East Asian (EAS) AF: 0.0266 AC: 138 AN: 5186

South Asian (SAS) AF: 0.384 AC: 1850 AN: 4822

European-Finnish (FIN) AF: 0.452 AC: 4772 AN: 10558

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28743 AN: 67978

Other (OTH) AF: 0.288 AC: 608 AN: 2108

Alfa AF: 0.373 Hom.: 40301

Bravo AF: 0.267

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.68
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs11616188; hg19: chr12-6502742;