10-6009144-C-T

Variant names:

• chr10-6009144-C-T
• rs12359875

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 0.162 in 152,148 control chromosomes in the GnomAD database, including 2,717 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 (2717 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 15 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 (NFE) allele frequency at 95% confidence interval = 0.238 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: 0.162 AC: 24650 AN: 152030 Hom.: 2716 Cov.: 32

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.162 AC: 24641 AN: 152148 Hom.: 2717 Cov.: 32 AF XY: 0.156 AC XY: 11612 AN XY: 74360

African (AFR) AF: 0.0461 AC: 1916 AN: 41530

American (AMR) AF: 0.157 AC: 2404 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 928 AN: 3466

East Asian (EAS) AF: 0.0146 AC: 76 AN: 5188

South Asian (SAS) AF: 0.129 AC: 622 AN: 4816

European-Finnish (FIN) AF: 0.132 AC: 1391 AN: 10576

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16390 AN: 67982

Other (OTH) AF: 0.193 AC: 407 AN: 2110

Alfa AF: 0.106 Hom.: 238

Bravo AF: 0.160

Asia WGS AF: 0.0750 AC: 261 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	1.0
DANN	Benign	0.71
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs12359875; hg19: chr10-6051107;