12-41795293-T-C

Variant names:

• chr12-41795293-T-C
• rs904075

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 0.941 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.928 AC: 38579 AN: 41582

American (AMR) AF: 0.950 AC: 14541 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3278 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5189 AN: 5190

South Asian (SAS) AF: 0.981 AC: 4735 AN: 4826

European-Finnish (FIN) AF: 0.958 AC: 10173 AN: 10620

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63738 AN: 68034

Other (OTH) AF: 0.939 AC: 1983 AN: 2112

Alfa AF: 0.938 Hom.: 34144

Bravo AF: 0.939

Asia WGS AF: 0.982 AC: 3415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.50
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs904075; hg19: chr12-42189095;