10-58952916-G-C

Variant names:

• chr10-58952916-G-C
• rs7089764

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 0.169 in 151,414 control chromosomes in the GnomAD database, including 2,414 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 0.17 (2414 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 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: 0.169 AC: 25524 AN: 151296 Hom.: 2412 Cov.: 30

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0812

Gnomad SAS AF: 0.0385

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.169 AC: 25549 AN: 151414 Hom.: 2414 Cov.: 30 AF XY: 0.167 AC XY: 12368 AN XY: 73916

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.0814

Gnomad4 SAS AF: 0.0379

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.155

Alfa AF: 0.0745 Hom.: 99

Bravo AF: 0.171

Asia WGS AF: 0.0870 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	12
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7089764; hg19: chr10-60712676;