chr10-34918225-C-T

Variant names:

• chr10-34918225-C-T
• rs11591754

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 0.168 in 152,076 control chromosomes in the GnomAD database, including 2,329 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 0.17 (2329 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 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: 0.168 AC: 25571 AN: 151958 Hom.: 2324 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.168 AC: 25585 AN: 152076 Hom.: 2329 Cov.: 32 AF XY: 0.171 AC XY: 12677 AN XY: 74316

African (AFR) AF: 0.100 AC: 4160 AN: 41520

American (AMR) AF: 0.203 AC: 3089 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 707 AN: 3472

East Asian (EAS) AF: 0.279 AC: 1435 AN: 5152

South Asian (SAS) AF: 0.214 AC: 1032 AN: 4816

European-Finnish (FIN) AF: 0.209 AC: 2205 AN: 10568

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12377 AN: 67982

Other (OTH) AF: 0.166 AC: 350 AN: 2110

Alfa AF: 0.177 Hom.: 6385

Bravo AF: 0.164

Asia WGS AF: 0.262 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.6
DANN	Benign	0.60
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs11591754; hg19: chr10-35207153;