rs7913244

chr10-10142402-T-Achr10-10142402-T-Cchr10-10142402-T-G

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 0.194 in 152,130 control chromosomes in the GnomAD database, including 3,520 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 0.19 (3520 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 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: 0.194 AC: 29498 AN: 152014 Hom.: 3505 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.0676

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.194 AC: 29560 AN: 152130 Hom.: 3520 Cov.: 32 AF XY: 0.197 AC XY: 14620 AN XY: 74366

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.0676

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.199

Alfa AF: 0.146 Hom.: 267

Bravo AF: 0.212

Asia WGS AF: 0.317 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.3
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7913244; hg19: chr10-10184365;