rs10744391

Variant names:

• chr12-128840393-G-A
• rs10744391

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 0.283 in 151,422 control chromosomes in the GnomAD database, including 6,151 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 0.28 (6151 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.414 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: 0.283 AC: 42805 AN: 151306 Hom.: 6137 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.283 AC: 42851 AN: 151422 Hom.: 6151 Cov.: 32 AF XY: 0.284 AC XY: 21000 AN XY: 73974

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.276

Alfa AF: 0.296 Hom.: 14509

Bravo AF: 0.272

Asia WGS AF: 0.270 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10744391; hg19: chr12-129324938;