rs17134158

Variant names:

• chr10-5022974-C-T
• rs17134158

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 0.243 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.199 AC: 8258 AN: 41534

American (AMR) AF: 0.265 AC: 4055 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 929 AN: 3472

East Asian (EAS) AF: 0.0598 AC: 310 AN: 5188

South Asian (SAS) AF: 0.250 AC: 1206 AN: 4820

European-Finnish (FIN) AF: 0.244 AC: 2579 AN: 10574

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18750 AN: 67990

Other (OTH) AF: 0.230 AC: 485 AN: 2112

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
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs17134158; hg19: chr10-5065166;