10-5025921-G-T

Variant names:

• chr10-5025921-G-T
• rs10904392

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 0.419 in 152,008 control chromosomes in the GnomAD database, including 13,935 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 (13935 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 8 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 (EAS) allele frequency at 95% confidence interval = 0.567 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: 0.419 AC: 63689 AN: 151888 Hom.: 13921 Cov.: 33

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.419 AC: 63747 AN: 152008 Hom.: 13935 Cov.: 33 AF XY: 0.418 AC XY: 31078 AN XY: 74302

African (AFR) AF: 0.526 AC: 21780 AN: 41428

American (AMR) AF: 0.341 AC: 5213 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1504 AN: 3470

East Asian (EAS) AF: 0.584 AC: 3017 AN: 5166

South Asian (SAS) AF: 0.511 AC: 2460 AN: 4810

European-Finnish (FIN) AF: 0.342 AC: 3616 AN: 10568

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24820 AN: 67960

Other (OTH) AF: 0.428 AC: 903 AN: 2112

Alfa AF: 0.382 Hom.: 34603

Bravo AF: 0.424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.7
DANN	Benign	0.76
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10904392; hg19: chr10-5068113;