rs11836346

chr12-63160185-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 0.264 in 152,130 control chromosomes in the GnomAD database, including 8,313 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 0.26 (8313 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 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: 0.264 AC: 40148 AN: 152010 Hom.: 8288 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0864

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.264 AC: 40216 AN: 152130 Hom.: 8313 Cov.: 32 AF XY: 0.261 AC XY: 19413 AN XY: 74380

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.0864

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.220

Alfa AF: 0.211 Hom.: 622

Bravo AF: 0.273

Asia WGS AF: 0.254 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.7
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11836346; hg19: chr12-63553965;