rs17134158

chr10-5022974-C-T

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 0.243 in 152,190 control chromosomes in the GnomAD database, including 4,654 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 0.24 (4654 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 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: 0.243 AC: 36932 AN: 152072 Hom.: 4651 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.0596

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.243 AC: 36974 AN: 152190 Hom.: 4654 Cov.: 33 AF XY: 0.242 AC XY: 17997 AN XY: 74394

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.0598

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.230

Alfa AF: 0.261 Hom.: 1026

Bravo AF: 0.241

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.0
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17134158; hg19: chr10-5065166;