rs10744816

Variant names:

• chr12-114276461-T-C
• rs10744816

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 0.389 in 152,044 control chromosomes in the GnomAD database, including 12,344 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 0.39 (12344 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59075 AN: 151926 Hom.: 12345 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.389 AC: 59108 AN: 152044 Hom.: 12344 Cov.: 32 AF XY: 0.381 AC XY: 28311 AN XY: 74316

African (AFR) AF: 0.254 AC: 10548 AN: 41480

American (AMR) AF: 0.355 AC: 5426 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1731 AN: 3464

East Asian (EAS) AF: 0.373 AC: 1925 AN: 5160

South Asian (SAS) AF: 0.326 AC: 1569 AN: 4810

European-Finnish (FIN) AF: 0.356 AC: 3769 AN: 10580

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32575 AN: 67954

Other (OTH) AF: 0.430 AC: 909 AN: 2114

Alfa AF: 0.448 Hom.: 42669

Bravo AF: 0.384

Asia WGS AF: 0.339 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.45
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs10744816; hg19: chr12-114714266;