10-123587871-A-T

Position:

• chr10-123587871-A-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 0.474 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;