rs11170547

chr12-53419219-C-T

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 0.0684 in 152,198 control chromosomes in the GnomAD database, including 497 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 0.068 (497 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 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: 0.0685 AC: 10417 AN: 152080 Hom.: 497 Cov.: 31

Gnomad AFR AF: 0.0183

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0541

Gnomad ASJ AF: 0.0896

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0385

Gnomad FIN AF: 0.0857

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0684 AC: 10417 AN: 152198 Hom.: 497 Cov.: 31 AF XY: 0.0666 AC XY: 4957 AN XY: 74414

Gnomad4 AFR AF: 0.0182

Gnomad4 AMR AF: 0.0540

Gnomad4 ASJ AF: 0.0896

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0388

Gnomad4 FIN AF: 0.0857

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0677

Alfa AF: 0.0981 Hom.: 740

Bravo AF: 0.0636

Asia WGS AF: 0.0170 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	4.5
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11170547; hg19: chr12-53813003;