rs7082598

Positions:

• chr10-119192212-C-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 0.112 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;