chr12-11367487-G-A

Position:

• chr12-11367487-G-A

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 0.554 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.552

Alfa AF: 0.612 Hom.: 5174

Asia WGS AF: 0.448 AC: 1540 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.98
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10845343; hg19: chr12-11520421;