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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0739

Gnomad4 AMR AF: 0.0176

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.0326

Gnomad4 FIN AF: 0.0271

Gnomad4 NFE AF: 0.0118

Gnomad4 OTH AF: 0.0317

Alfa AF: 0.0134 Hom.: 53

Bravo AF: 0.0370

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517488; hg19: chr4-60918911;