rs10488593

Variant names:

• chr7-84494166-C-T
• rs10488593

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 0.0134 in 151,864 control chromosomes in the GnomAD database, including 97 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 0.013 (97 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

ACMG classification

Verdict is Benign. Variant got -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 = 0.149 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: 0.0135 AC: 2041 AN: 151746 Hom.: 97 Cov.: 32

Gnomad AFR AF: 0.00167

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0412

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.0102

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00393

Gnomad OTH AF: 0.0168

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

GnomAD4 genome AF: 0.0134 AC: 2037 AN: 151864 Hom.: 97 Cov.: 32 AF XY: 0.0150 AC XY: 1113 AN XY: 74208

Gnomad4 AFR AF: 0.00166

Gnomad4 AMR AF: 0.0410

Gnomad4 ASJ AF: 0.0196

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.0104

Gnomad4 FIN AF: 0.0102

Gnomad4 NFE AF: 0.00393

Gnomad4 OTH AF: 0.0162

Alfa AF: 0.00836 Hom.: 4

Bravo AF: 0.0166

Asia WGS AF: 0.0730 AC: 251 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.031
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488593; hg19: chr7-84123482;