10-123587871-A-T

Variant names:

• chr10-123587871-A-T
• rs859510

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 0.474 in 152,004 control chromosomes in the GnomAD database, including 17,865 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 0.47 (17865 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 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: 0.474 AC: 71979 AN: 151886 Hom.: 17856 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.474 AC: 72023 AN: 152004 Hom.: 17865 Cov.: 32 AF XY: 0.480 AC XY: 35648 AN XY: 74300

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.490

Alfa AF: 0.475 Hom.: 2173

Bravo AF: 0.472

Asia WGS AF: 0.658 AC: 2289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs859510; hg19: chr10-125347387;