10-52818498-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 0.164 in 152,012 control chromosomes in the GnomAD database, including 2,611 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 0.16 (2611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24920 AN: 151894 Hom.: 2606 Cov.: 32

Gnomad AFR AF: 0.0442

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.164 AC: 24924 AN: 152012 Hom.: 2611 Cov.: 32 AF XY: 0.168 AC XY: 12459 AN XY: 74294

Gnomad4 AFR AF: 0.0441

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.174

Alfa AF: 0.177 Hom.: 332

Bravo AF: 0.168

Asia WGS AF: 0.185 AC: 645 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.4
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11819277; hg19: chr10-54578258;