10-52773600-A-G

Variant names:

• chr10-52773600-A-G
• rs1031101

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 0.116 in 152,174 control chromosomes in the GnomAD database, including 1,256 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 0.12 (1256 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.168 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: 0.116 AC: 17697 AN: 152056 Hom.: 1252 Cov.: 32

Gnomad AFR AF: 0.0317

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.116 AC: 17705 AN: 152174 Hom.: 1256 Cov.: 32 AF XY: 0.119 AC XY: 8856 AN XY: 74414

African (AFR) AF: 0.0317 AC: 1316 AN: 41540

American (AMR) AF: 0.173 AC: 2650 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 519 AN: 3464

East Asian (EAS) AF: 0.170 AC: 875 AN: 5162

South Asian (SAS) AF: 0.136 AC: 657 AN: 4818

European-Finnish (FIN) AF: 0.147 AC: 1558 AN: 10596

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9653 AN: 67988

Other (OTH) AF: 0.124 AC: 261 AN: 2110

Alfa AF: 0.126 Hom.: 388

Bravo AF: 0.116

Asia WGS AF: 0.142 AC: 497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.61
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1031101; hg19: chr10-54533360;