12-41795293-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 0.941 in 152,350 control chromosomes in the GnomAD database, including 67,507 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 0.94 (67507 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.848

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.941 AC: 143262 AN: 152232 Hom.: 67451 Cov.: 34

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.981

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.941 AC: 143375 AN: 152350 Hom.: 67507 Cov.: 34 AF XY: 0.944 AC XY: 70328 AN XY: 74494

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.950

Gnomad4 ASJ AF: 0.944

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.981

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.937

Gnomad4 OTH AF: 0.939

Alfa AF: 0.938 Hom.: 30436

Bravo AF: 0.939

Asia WGS AF: 0.982 AC: 3415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	13
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs904075; hg19: chr12-42189095;