rs17154929

Variant names:

• chr10-44029227-C-T
• rs17154929

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 0.0249 in 152,186 control chromosomes in the GnomAD database, including 125 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 0.025 (125 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.108 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: 0.0249 AC: 3793 AN: 152068 Hom.: 123 Cov.: 32

Gnomad AFR AF: 0.00456

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0668

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0135

Gnomad OTH AF: 0.0201

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

GnomAD4 genome AF: 0.0249 AC: 3792 AN: 152186 Hom.: 125 Cov.: 32 AF XY: 0.0292 AC XY: 2170 AN XY: 74390

Gnomad4 AFR AF: 0.00455

Gnomad4 AMR AF: 0.0673

Gnomad4 ASJ AF: 0.00893

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.0702

Gnomad4 FIN AF: 0.0562

Gnomad4 NFE AF: 0.0135

Gnomad4 OTH AF: 0.0185

Alfa AF: 0.0164 Hom.: 37

Bravo AF: 0.0243

Asia WGS AF: 0.0820 AC: 287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.46
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17154929; hg19: chr10-44524675;