10-1923743-G-A

Variant names:

• chr10-1923743-G-A
• rs1029182

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 0.607 in 151,862 control chromosomes in the GnomAD database, including 28,427 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 0.61 (28427 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 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: 0.607 AC: 92115 AN: 151744 Hom.: 28425 Cov.: 31

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.607 AC: 92151 AN: 151862 Hom.: 28427 Cov.: 31 AF XY: 0.607 AC XY: 45062 AN XY: 74220

African (AFR) AF: 0.509 AC: 21073 AN: 41376

American (AMR) AF: 0.614 AC: 9372 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2809 AN: 3470

East Asian (EAS) AF: 0.532 AC: 2730 AN: 5134

South Asian (SAS) AF: 0.605 AC: 2917 AN: 4820

European-Finnish (FIN) AF: 0.678 AC: 7155 AN: 10552

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43965 AN: 67932

Other (OTH) AF: 0.630 AC: 1331 AN: 2114

Alfa AF: 0.639 Hom.: 83030

Bravo AF: 0.600

Asia WGS AF: 0.533 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.52
DANN	Benign	0.44
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1029182; hg19: chr10-1965937;