chr10-17134826-C-T

Variant names:

• chr10-17134826-C-T
• rs11254389

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 0.115 in 152,110 control chromosomes in the GnomAD database, including 1,275 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 0.12 (1275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.158 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: 0.116 AC: 17572 AN: 151992 Hom.: 1275 Cov.: 32

Gnomad AFR AF: 0.0339

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0802

Gnomad EAS AF: 0.0364

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.115 AC: 17565 AN: 152110 Hom.: 1275 Cov.: 32 AF XY: 0.116 AC XY: 8620 AN XY: 74332

African (AFR) AF: 0.0338 AC: 1401 AN: 41496

American (AMR) AF: 0.163 AC: 2490 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0802 AC: 278 AN: 3468

East Asian (EAS) AF: 0.0359 AC: 186 AN: 5182

South Asian (SAS) AF: 0.105 AC: 505 AN: 4822

European-Finnish (FIN) AF: 0.180 AC: 1896 AN: 10552

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.152 AC: 10346 AN: 68000

Other (OTH) AF: 0.131 AC: 276 AN: 2108

Alfa AF: 0.131 Hom.: 485

Bravo AF: 0.112

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.20
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs11254389; hg19: chr10-17176825;