12-41795293-T-C

Variant names:

• chr12-41795293-T-C
• rs904075

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;