rs10744676

chr12-5043783-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.881 in 152,100 control chromosomes in the GnomAD database, including 59,152 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.88 (59152 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.57

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 12-5043783-C-T is Benign according to our data. Variant chr12-5043783-C-T is described in ClinVar as [Benign]. Clinvar id is 1277403.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.881 AC: 133933 AN: 151982 Hom.: 59113 Cov.: 32

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.885

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

GnomAD4 genome AF: 0.881 AC: 134029 AN: 152100 Hom.: 59152 Cov.: 32 AF XY: 0.884 AC XY: 65700 AN XY: 74362

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.903

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.886

Alfa AF: 0.871 Hom.: 7159

Bravo AF: 0.882

Asia WGS AF: 0.956 AC: 3325 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 04, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.77
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10744676; hg19: chr12-5152949; COSMIC: COSV52907332;