rs10517488

Variant names:

• chr4-60053193-G-A
• rs10517488

Your query was ambiguous. Multiple possible variants found:

• chr4-60053193-G-A
• chr4-60053193-G-C
• chr4-60053193-G-T

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 0.0358 in 152,038 control chromosomes in the GnomAD database, including 189 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 0.036 (189 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.141 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: 0.0356 AC: 5406 AN: 151920 Hom.: 184 Cov.: 32

Gnomad AFR AF: 0.0734

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0177

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0326

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0358 AC: 5437 AN: 152038 Hom.: 189 Cov.: 32 AF XY: 0.0362 AC XY: 2694 AN XY: 74320

African (AFR) AF: 0.0739 AC: 3069 AN: 41510

American (AMR) AF: 0.0176 AC: 269 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3468

East Asian (EAS) AF: 0.150 AC: 773 AN: 5168

South Asian (SAS) AF: 0.0326 AC: 157 AN: 4818

European-Finnish (FIN) AF: 0.0271 AC: 287 AN: 10606

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0118 AC: 803 AN: 67908

Other (OTH) AF: 0.0317 AC: 67 AN: 2112

Alfa AF: 0.0194 Hom.: 163

Bravo AF: 0.0370

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.79
DANN	Benign	0.33
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs10517488; hg19: chr4-60918911;