chr10-59376457-T-G

Variant names:

• chr10-59376457-T-G
• rs384626

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 0.586 in 151,856 control chromosomes in the GnomAD database, including 27,486 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 0.59 (27486 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88808 AN: 151738 Hom.: 27421 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.586 AC: 88938 AN: 151856 Hom.: 27486 Cov.: 32 AF XY: 0.585 AC XY: 43390 AN XY: 74192

African (AFR) AF: 0.792 AC: 32804 AN: 41442

American (AMR) AF: 0.630 AC: 9602 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1638 AN: 3468

East Asian (EAS) AF: 0.442 AC: 2269 AN: 5132

South Asian (SAS) AF: 0.551 AC: 2653 AN: 4818

European-Finnish (FIN) AF: 0.490 AC: 5166 AN: 10540

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33110 AN: 67902

Other (OTH) AF: 0.545 AC: 1151 AN: 2110

Alfa AF: 0.528 Hom.: 28831

Bravo AF: 0.606

Asia WGS AF: 0.548 AC: 1906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.2
DANN	Benign	0.80
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs384626; hg19: chr10-61136215; COSMIC: COSV69461209;