chr10-52342245-A-C

Variant names:

• chr10-52342245-A-C
• rs1528873

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 0.418 in 152,032 control chromosomes in the GnomAD database, including 13,779 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 0.42 (13779 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 10 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 (NFE) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63485 AN: 151912 Hom.: 13773 Cov.: 33

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.418 AC: 63505 AN: 152032 Hom.: 13779 Cov.: 33 AF XY: 0.415 AC XY: 30816 AN XY: 74292

African (AFR) AF: 0.342 AC: 14161 AN: 41466

American (AMR) AF: 0.416 AC: 6360 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2096 AN: 3470

East Asian (EAS) AF: 0.193 AC: 995 AN: 5164

South Asian (SAS) AF: 0.312 AC: 1507 AN: 4828

European-Finnish (FIN) AF: 0.442 AC: 4656 AN: 10542

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32243 AN: 67964

Other (OTH) AF: 0.439 AC: 928 AN: 2112

Alfa AF: 0.463 Hom.: 22023

Bravo AF: 0.414

Asia WGS AF: 0.227 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.84
DANN	Benign	0.77
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1528873; hg19: chr10-54102005;