chr10-1854361-G-A

Variant names:

• chr10-1854361-G-A
• rs10794792

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 0.578 in 151,944 control chromosomes in the GnomAD database, including 26,525 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 0.58 (26525 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 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: 0.578 AC: 87827 AN: 151826 Hom.: 26509 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.578 AC: 87892 AN: 151944 Hom.: 26525 Cov.: 32 AF XY: 0.580 AC XY: 43086 AN XY: 74256

African (AFR) AF: 0.392 AC: 16233 AN: 41400

American (AMR) AF: 0.575 AC: 8779 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2166 AN: 3466

East Asian (EAS) AF: 0.561 AC: 2888 AN: 5148

South Asian (SAS) AF: 0.594 AC: 2853 AN: 4806

European-Finnish (FIN) AF: 0.660 AC: 6972 AN: 10566

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45894 AN: 67978

Other (OTH) AF: 0.594 AC: 1256 AN: 2114

Alfa AF: 0.649 Hom.: 19008

Bravo AF: 0.565

Asia WGS AF: 0.572 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.60
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10794792; hg19: chr10-1896555;