rs17128356

Variant names:

• chr10-111072467-C-T
• rs17128356

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 0.0865 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
• Publications: 7 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.169 AC: 6749 AN: 39944

American (AMR) AF: 0.0623 AC: 914 AN: 14676

Ashkenazi Jewish (ASJ) AF: 0.0407 AC: 139 AN: 3416

East Asian (EAS) AF: 0.197 AC: 955 AN: 4842

South Asian (SAS) AF: 0.145 AC: 650 AN: 4476

European-Finnish (FIN) AF: 0.00595 AC: 57 AN: 9580

Middle Eastern (MID) AF: 0.0810 AC: 23 AN: 284

European-Non Finnish (NFE) AF: 0.0454 AC: 3043 AN: 66998

Other (OTH) AF: 0.0754 AC: 154 AN: 2042

Alfa AF: 0.0592 Hom.: 662

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
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs17128356; hg19: chr10-112832225;