10-90318940-C-T

Variant names:

• chr10-90318940-C-T
• rs2104483

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 0.251 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0826 AC: 3429 AN: 41496

American (AMR) AF: 0.391 AC: 5964 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 917 AN: 3470

East Asian (EAS) AF: 0.964 AC: 4980 AN: 5168

South Asian (SAS) AF: 0.440 AC: 2122 AN: 4818

European-Finnish (FIN) AF: 0.385 AC: 4064 AN: 10546

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15980 AN: 67958

Other (OTH) AF: 0.251 AC: 530 AN: 2108

Alfa AF: 0.239 Hom.: 8259

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
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2104483; hg19: chr10-92078697;