10-92703125-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;