10-7694941-C-T

Variant names:

• chr10-7694941-C-T
• rs11255291

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.4 in 151,956 control chromosomes in the GnomAD database, including 12,776 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 0.40 (12776 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.492 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: 0.400 AC: 60794 AN: 151838 Hom.: 12766 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.400 AC: 60848 AN: 151956 Hom.: 12776 Cov.: 32 AF XY: 0.399 AC XY: 29633 AN XY: 74268

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.397

Alfa AF: 0.430 Hom.: 12223

Bravo AF: 0.406

Asia WGS AF: 0.324 AC: 1130 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	0.49
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11255291; hg19: chr10-7736904;