10-90318940-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 0.251 in 152,026 control chromosomes in the GnomAD database, including 7,139 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 0.25 (7139 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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: 0.251 AC: 38190 AN: 151908 Hom.: 7130 Cov.: 32

Gnomad AFR AF: 0.0825

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.251 AC: 38223 AN: 152026 Hom.: 7139 Cov.: 32 AF XY: 0.269 AC XY: 20011 AN XY: 74342

Gnomad4 AFR AF: 0.0826

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.251

Alfa AF: 0.242 Hom.: 6673

Bravo AF: 0.246

Asia WGS AF: 0.622 AC: 2163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.1
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2104483; hg19: chr10-92078697;