10-59543289-C-T

Variant names:

• chr10-59543289-C-T
• rs10509106

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 0.0803 in 152,140 control chromosomes in the GnomAD database, including 643 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 0.080 (643 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 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: 0.0804 AC: 12217 AN: 152020 Hom.: 643 Cov.: 32

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.0709

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

GnomAD4 genome AF: 0.0803 AC: 12223 AN: 152140 Hom.: 643 Cov.: 32 AF XY: 0.0839 AC XY: 6243 AN XY: 74366

African (AFR) AF: 0.0189 AC: 783 AN: 41522

American (AMR) AF: 0.0772 AC: 1179 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 432 AN: 3466

East Asian (EAS) AF: 0.179 AC: 928 AN: 5178

South Asian (SAS) AF: 0.195 AC: 938 AN: 4812

European-Finnish (FIN) AF: 0.131 AC: 1390 AN: 10582

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.0925 AC: 6292 AN: 67996

Other (OTH) AF: 0.0697 AC: 147 AN: 2108

Alfa AF: 0.0914 Hom.: 423

Bravo AF: 0.0729

Asia WGS AF: 0.147 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.64
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10509106; hg19: chr10-61303047;