rs11611647

chr12-4224753-T-C

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 0.221 in 152,204 control chromosomes in the GnomAD database, including 3,811 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 0.22 (3811 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 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: 0.220 AC: 33516 AN: 152086 Hom.: 3805 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.221 AC: 33562 AN: 152204 Hom.: 3811 Cov.: 32 AF XY: 0.222 AC XY: 16522 AN XY: 74420

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.235

Alfa AF: 0.212 Hom.: 5210

Bravo AF: 0.223

Asia WGS AF: 0.195 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.7
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11611647; hg19: chr12-4333919;