chr10-113989376-G-T

Variant names:

• chr10-113989376-G-T
• rs6585258

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 0.452 in 151,578 control chromosomes in the GnomAD database, including 15,620 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 0.45 (15620 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 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: 0.452 AC: 68458 AN: 151460 Hom.: 15604 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.452 AC: 68521 AN: 151578 Hom.: 15620 Cov.: 32 AF XY: 0.455 AC XY: 33699 AN XY: 74058

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.436

Alfa AF: 0.436 Hom.: 6508

Bravo AF: 0.451

Asia WGS AF: 0.474 AC: 1617 AN: 3416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6585258; hg19: chr10-115749135;