chr10-73973541-A-G

Variant names:

• chr10-73973541-A-G
• rs11000828

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 0.416 in 152,044 control chromosomes in the GnomAD database, including 14,547 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 (14547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 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: 0.416 AC: 63272 AN: 151926 Hom.: 14548 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.0366

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.416 AC: 63273 AN: 152044 Hom.: 14547 Cov.: 32 AF XY: 0.405 AC XY: 30099 AN XY: 74330

African (AFR) AF: 0.282 AC: 11688 AN: 41448

American (AMR) AF: 0.460 AC: 7027 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3470

East Asian (EAS) AF: 0.0363 AC: 188 AN: 5180

South Asian (SAS) AF: 0.230 AC: 1108 AN: 4826

European-Finnish (FIN) AF: 0.380 AC: 4017 AN: 10578

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35889 AN: 67956

Other (OTH) AF: 0.456 AC: 963 AN: 2110

Alfa AF: 0.502 Hom.: 32489

Bravo AF: 0.418

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.99
DANN	Benign	0.62
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs11000828; hg19: chr10-75733299;