chr10-132482311-C-T

Variant names:

• chr10-132482311-C-T
• rs73389468

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 0.123 in 152,154 control chromosomes in the GnomAD database, including 2,833 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 (2833 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 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: 0.123 AC: 18725 AN: 152036 Hom.: 2817 Cov.: 33

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.0530

Gnomad EAS AF: 0.0585

Gnomad SAS AF: 0.0692

Gnomad FIN AF: 0.00452

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0213

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.123 AC: 18775 AN: 152154 Hom.: 2833 Cov.: 33 AF XY: 0.119 AC XY: 8866 AN XY: 74404

African (AFR) AF: 0.364 AC: 15065 AN: 41444

American (AMR) AF: 0.0711 AC: 1088 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0530 AC: 184 AN: 3470

East Asian (EAS) AF: 0.0589 AC: 304 AN: 5164

South Asian (SAS) AF: 0.0686 AC: 331 AN: 4826

European-Finnish (FIN) AF: 0.00452 AC: 48 AN: 10612

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0213 AC: 1447 AN: 68022

Other (OTH) AF: 0.112 AC: 237 AN: 2114

Alfa AF: 0.0662 Hom.: 210

Bravo AF: 0.138

Asia WGS AF: 0.0780 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.56
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs73389468; hg19: chr10-134295815;