10-53506471-T-G

Variant names:

• chr10-53506471-T-G
• rs10825036

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 0.214 in 151,844 control chromosomes in the GnomAD database, including 4,379 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 0.21 (4379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32532 AN: 151726 Hom.: 4382 Cov.: 32

Gnomad AFR AF: 0.0539

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.214 AC: 32527 AN: 151844 Hom.: 4379 Cov.: 32 AF XY: 0.215 AC XY: 15934 AN XY: 74210

African (AFR) AF: 0.0537 AC: 2232 AN: 41526

American (AMR) AF: 0.165 AC: 2511 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 980 AN: 3462

East Asian (EAS) AF: 0.273 AC: 1407 AN: 5158

South Asian (SAS) AF: 0.267 AC: 1286 AN: 4814

European-Finnish (FIN) AF: 0.307 AC: 3236 AN: 10542

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.297 AC: 20143 AN: 67770

Other (OTH) AF: 0.223 AC: 470 AN: 2110

Alfa AF: 0.249 Hom.: 695

Bravo AF: 0.196

Asia WGS AF: 0.253 AC: 871 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.4
DANN	Benign	0.82
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10825036; hg19: chr10-55266231; COSMIC: COSV66524257;