10-52388529-A-T

Variant names:

• chr10-52388529-A-T
• rs1194669

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 0.598 in 151,996 control chromosomes in the GnomAD database, including 28,523 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 0.60 (28523 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.807 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: 0.598 AC: 90811 AN: 151878 Hom.: 28489 Cov.: 31

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.598 AC: 90900 AN: 151996 Hom.: 28523 Cov.: 31 AF XY: 0.594 AC XY: 44150 AN XY: 74308

African (AFR) AF: 0.779 AC: 32334 AN: 41502

American (AMR) AF: 0.551 AC: 8410 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1433 AN: 3468

East Asian (EAS) AF: 0.828 AC: 4277 AN: 5168

South Asian (SAS) AF: 0.447 AC: 2156 AN: 4818

European-Finnish (FIN) AF: 0.531 AC: 5609 AN: 10562

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34958 AN: 67904

Other (OTH) AF: 0.548 AC: 1158 AN: 2112

Alfa AF: 0.569 Hom.: 3157

Bravo AF: 0.608

Asia WGS AF: 0.672 AC: 2332 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs1194669; hg19: chr10-54148289;