chr1-185417483-C-T

Variant names:

• chr1-185417483-C-T
• rs10489482

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 0.407 in 151,938 control chromosomes in the GnomAD database, including 14,295 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 0.41 (14295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 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: 0.407 AC: 61772 AN: 151820 Hom.: 14246 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.407 AC: 61881 AN: 151938 Hom.: 14295 Cov.: 32 AF XY: 0.408 AC XY: 30257 AN XY: 74232

African (AFR) AF: 0.633 AC: 26208 AN: 41420

American (AMR) AF: 0.460 AC: 7029 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3470

East Asian (EAS) AF: 0.391 AC: 2017 AN: 5164

South Asian (SAS) AF: 0.383 AC: 1847 AN: 4826

European-Finnish (FIN) AF: 0.259 AC: 2721 AN: 10520

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.291 AC: 19759 AN: 67958

Other (OTH) AF: 0.360 AC: 759 AN: 2110

Alfa AF: 0.326 Hom.: 17122

Bravo AF: 0.434

Asia WGS AF: 0.352 AC: 1227 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.55
DANN	Benign	0.58
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs10489482; hg19: chr1-185386615;