rs11616188

Positions:

• chr12-6393576-G-A

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 0.298 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0882

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.0266

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.288

Alfa AF: 0.387 Hom.: 16263

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11616188; hg19: chr12-6502742;