rs1932571

Variant names:

• chr10-80001733-C-T
• rs1932571

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 0.232 in 152,118 control chromosomes in the GnomAD database, including 4,502 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 0.23 (4502 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856
• 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 = 0.387 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35293 AN: 152000 Hom.: 4486 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.0994

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.232 AC: 35342 AN: 152118 Hom.: 4502 Cov.: 33 AF XY: 0.235 AC XY: 17492 AN XY: 74368

African (AFR) AF: 0.272 AC: 11289 AN: 41480

American (AMR) AF: 0.312 AC: 4760 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1137 AN: 3470

East Asian (EAS) AF: 0.401 AC: 2074 AN: 5170

South Asian (SAS) AF: 0.330 AC: 1587 AN: 4816

European-Finnish (FIN) AF: 0.0994 AC: 1054 AN: 10600

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12669 AN: 68002

Other (OTH) AF: 0.264 AC: 557 AN: 2112

Alfa AF: 0.212 Hom.: 6103

Bravo AF: 0.247

Asia WGS AF: 0.359 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.52
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs1932571; hg19: chr10-81761489;