rs10422744

Variant names:

• chr19-35356251-C-T
• rs10422744

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 0.42 in 151,738 control chromosomes in the GnomAD database, including 13,548 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 0.42 (13548 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 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: 0.420 AC: 63681 AN: 151620 Hom.: 13542 Cov.: 30

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.420 AC: 63720 AN: 151738 Hom.: 13548 Cov.: 30 AF XY: 0.422 AC XY: 31282 AN XY: 74152

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.428

Alfa AF: 0.400 Hom.: 9016

Bravo AF: 0.422

Asia WGS AF: 0.472 AC: 1638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10422744; hg19: chr19-35847153;