rs17154929

Variant names:

• chr10-44029227-C-T
• rs17154929

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 0.0249 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.00455 AC: 189 AN: 41550

American (AMR) AF: 0.0673 AC: 1029 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00893 AC: 31 AN: 3470

East Asian (EAS) AF: 0.115 AC: 594 AN: 5148

South Asian (SAS) AF: 0.0702 AC: 338 AN: 4818

European-Finnish (FIN) AF: 0.0562 AC: 595 AN: 10588

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0135 AC: 918 AN: 68000

Other (OTH) AF: 0.0185 AC: 39 AN: 2112

Alfa AF: 0.0172 Hom.: 141

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
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs17154929; hg19: chr10-44524675;