12-83740041-C-T

Variant names:

• chr12-83740041-C-T
• rs717996

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 0.682 in 152,064 control chromosomes in the GnomAD database, including 36,420 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 0.68 (36420 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 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: 0.682 AC: 103602 AN: 151946 Hom.: 36378 Cov.: 33

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.682 AC: 103702 AN: 152064 Hom.: 36420 Cov.: 33 AF XY: 0.680 AC XY: 50536 AN XY: 74316

African (AFR) AF: 0.804 AC: 33387 AN: 41518

American (AMR) AF: 0.790 AC: 12077 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2605 AN: 3468

East Asian (EAS) AF: 0.724 AC: 3741 AN: 5164

South Asian (SAS) AF: 0.790 AC: 3807 AN: 4820

European-Finnish (FIN) AF: 0.451 AC: 4751 AN: 10534

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40970 AN: 67958

Other (OTH) AF: 0.711 AC: 1504 AN: 2116

Alfa AF: 0.639 Hom.: 96959

Bravo AF: 0.716

Asia WGS AF: 0.713 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.5
DANN	Benign	0.68
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs717996; hg19: chr12-84133820; COSMIC: COSV53403070;