rs17110999

Variant names:

• chr10-95588103-T-C
• rs17110999

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 0.159 in 152,028 control chromosomes in the GnomAD database, including 2,111 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 0.16 (2111 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.188 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: 0.159 AC: 24191 AN: 151906 Hom.: 2107 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.0984

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.159 AC: 24217 AN: 152028 Hom.: 2111 Cov.: 32 AF XY: 0.158 AC XY: 11749 AN XY: 74300

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.0984

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.195

Alfa AF: 0.148 Hom.: 462

Bravo AF: 0.162

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.6
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17110999; hg19: chr10-97347860;