12-11367487-G-A

Variant names:

• chr12-11367487-G-A
• rs10845343

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 0.554 in 147,354 control chromosomes in the GnomAD database, including 24,788 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 0.55 (24788 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.554 AC: 81582 AN: 147236 Hom.: 24771 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.554 AC: 81642 AN: 147354 Hom.: 24788 Cov.: 32 AF XY: 0.551 AC XY: 39574 AN XY: 71848

African (AFR) AF: 0.388 AC: 15100 AN: 38954

American (AMR) AF: 0.540 AC: 7982 AN: 14794

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2148 AN: 3444

East Asian (EAS) AF: 0.402 AC: 2047 AN: 5092

South Asian (SAS) AF: 0.475 AC: 2241 AN: 4716

European-Finnish (FIN) AF: 0.672 AC: 6810 AN: 10136

Middle Eastern (MID) AF: 0.607 AC: 176 AN: 290

European-Non Finnish (NFE) AF: 0.648 AC: 43416 AN: 66986

Other (OTH) AF: 0.552 AC: 1124 AN: 2036

Alfa AF: 0.617 Hom.: 6734

Asia WGS AF: 0.448 AC: 1540 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.98
DANN	Benign	0.30
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10845343; hg19: chr12-11520421;