rs11170547

Variant names:

• chr12-53419219-C-T
• rs11170547

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 0.0684 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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0182 AC: 756 AN: 41528

American (AMR) AF: 0.0540 AC: 825 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0896 AC: 311 AN: 3470

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5188

South Asian (SAS) AF: 0.0388 AC: 187 AN: 4824

European-Finnish (FIN) AF: 0.0857 AC: 907 AN: 10588

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7215 AN: 68000

Other (OTH) AF: 0.0677 AC: 143 AN: 2112

Alfa AF: 0.0922 Hom.: 1011

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
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs11170547; hg19: chr12-53813003;