10-119485227-T-C

Variant names:

• chr10-119485227-T-C
• rs2039488

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 0.117 in 152,234 control chromosomes in the GnomAD database, including 1,308 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 0.12 (1308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.687
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 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: 0.117 AC: 17801 AN: 152116 Hom.: 1307 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0867

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.117 AC: 17805 AN: 152234 Hom.: 1308 Cov.: 32 AF XY: 0.116 AC XY: 8634 AN XY: 74422

African (AFR) AF: 0.171 AC: 7119 AN: 41538

American (AMR) AF: 0.105 AC: 1605 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 360 AN: 3470

East Asian (EAS) AF: 0.278 AC: 1438 AN: 5170

South Asian (SAS) AF: 0.138 AC: 667 AN: 4824

European-Finnish (FIN) AF: 0.0385 AC: 409 AN: 10622

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0867 AC: 5899 AN: 68008

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.100 Hom.: 2669

Bravo AF: 0.127

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.4
DANN	Benign	0.55
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs2039488; hg19: chr10-121244739;