10-92703125-C-T

Variant names:

• chr10-92703125-C-T
• rs1111875

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 0.371 in 152,048 control chromosomes in the GnomAD database, including 11,515 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 0.37 (11515 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 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: 0.372 AC: 56465 AN: 151930 Hom.: 11518 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.371 AC: 56481 AN: 152048 Hom.: 11515 Cov.: 32 AF XY: 0.377 AC XY: 28014 AN XY: 74344

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.366

Alfa AF: 0.400 Hom.: 7197

Bravo AF: 0.354

Asia WGS AF: 0.582 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1111875; hg19: chr10-94462882;