rs7082598

Variant names:

• chr10-119192212-C-T
• rs7082598

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 0.112 in 148,232 control chromosomes in the GnomAD database, including 1,030 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 0.11 (1030 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 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: 0.112 AC: 16607 AN: 148134 Hom.: 1029 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0939

Gnomad EAS AF: 0.0330

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.112 AC: 16608 AN: 148232 Hom.: 1030 Cov.: 31 AF XY: 0.111 AC XY: 8068 AN XY: 72478

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.0939

Gnomad4 EAS AF: 0.0331

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0771

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.108

Alfa AF: 0.102 Hom.: 93

Bravo AF: 0.112

Asia WGS AF: 0.0770 AC: 270 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7082598; hg19: chr10-120951724;