rs17128356

Positions:

• chr10-111072467-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 0.0865 in 147,152 control chromosomes in the GnomAD database, including 830 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 0.087 (830 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 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: 0.0866 AC: 12735 AN: 147042 Hom.: 829 Cov.: 29

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.0624

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.00595

Gnomad MID AF: 0.0855

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0757

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

GnomAD4 genome AF: 0.0866 AC: 12736 AN: 147152 Hom.: 830 Cov.: 29 AF XY: 0.0858 AC XY: 6134 AN XY: 71500

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0623

Gnomad4 ASJ AF: 0.0407

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.00595

Gnomad4 NFE AF: 0.0454

Gnomad4 OTH AF: 0.0754

Alfa AF: 0.0563 Hom.: 463

Bravo AF: 0.0918

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17128356; hg19: chr10-112832225;