rs7082598

Variant names:

• chr10-119192212-C-T
• rs7082598
• ENST00000826909.1:n.258+11758C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000826909.1(ENSG00000307533):​n.258+11758C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000307533 ENST00000826909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 7 publications found

Genes affected

ENSG00000307533 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826909.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307533	ENST00000826909.1		n.258+11758C>T		intron	N/A
	ENSG00000307533	ENST00000826910.1		n.137-10393C>T		intron	N/A

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

African (AFR) AF: 0.147 AC: 5594 AN: 37960

American (AMR) AF: 0.125 AC: 1888 AN: 15072

Ashkenazi Jewish (ASJ) AF: 0.0939 AC: 326 AN: 3470

East Asian (EAS) AF: 0.0331 AC: 171 AN: 5168

South Asian (SAS) AF: 0.133 AC: 640 AN: 4806

European-Finnish (FIN) AF: 0.0771 AC: 814 AN: 10564

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.101 AC: 6853 AN: 67934

Other (OTH) AF: 0.108 AC: 222 AN: 2056

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.49
PhyloP100		-0.11

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7082598;

hg19: chr10-120951724;