rs10479200

Variant names:

• chr5-102336534-T-G
• rs10479200

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 0.197 in 151,742 control chromosomes in the GnomAD database, including 4,010 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 0.20 (4010 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 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: 0.197 AC: 29841 AN: 151624 Hom.: 4013 Cov.: 32

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0312

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.197 AC: 29831 AN: 151742 Hom.: 4010 Cov.: 32 AF XY: 0.202 AC XY: 14981 AN XY: 74152

African (AFR) AF: 0.0442 AC: 1834 AN: 41486

American (AMR) AF: 0.188 AC: 2860 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1197 AN: 3466

East Asian (EAS) AF: 0.0313 AC: 162 AN: 5178

South Asian (SAS) AF: 0.145 AC: 701 AN: 4818

European-Finnish (FIN) AF: 0.401 AC: 4220 AN: 10530

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18093 AN: 67728

Other (OTH) AF: 0.225 AC: 473 AN: 2100

Alfa AF: 0.206 Hom.: 2700

Bravo AF: 0.175

Asia WGS AF: 0.0910 AC: 318 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.68
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10479200; hg19: chr5-101672238;