rs1873800

Variant names:

• chr10-56605655-T-C
• rs1873800

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 0.447 in 151,898 control chromosomes in the GnomAD database, including 15,855 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 0.45 (15855 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67817 AN: 151778 Hom.: 15841 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.447 AC: 67869 AN: 151898 Hom.: 15855 Cov.: 32 AF XY: 0.443 AC XY: 32893 AN XY: 74232

African (AFR) AF: 0.574 AC: 23767 AN: 41378

American (AMR) AF: 0.347 AC: 5296 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1024 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1526 AN: 5152

South Asian (SAS) AF: 0.370 AC: 1782 AN: 4818

European-Finnish (FIN) AF: 0.441 AC: 4649 AN: 10542

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28406 AN: 67952

Other (OTH) AF: 0.410 AC: 864 AN: 2108

Alfa AF: 0.421 Hom.: 37777

Bravo AF: 0.445

Asia WGS AF: 0.372 AC: 1295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.93
DANN	Benign	0.51
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1873800; hg19: chr10-58365415;