ENST00000783190.1:n.210-13086T>C

Variant names:

• chr10-58833048-A-G
• rs7098555
• ENST00000783190.1:n.210-13086T>C

Variant summary

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

The ENST00000783190.1(ENSG00000301981):​n.210-13086T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,114 control chromosomes in the GnomAD database, including 50,271 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 0.79 (50271 hom., cov: 32)
• Consequence: ENSG00000301981 ENST00000783190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388
• Publications: 2 publications found

Genes affected

ENSG00000301981 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783190.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301981	ENST00000783190.1		n.210-13086T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.790 AC: 120113 AN: 151996 Hom.: 50262 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.790 AC: 120155 AN: 152114 Hom.: 50271 Cov.: 32 AF XY: 0.790 AC XY: 58778 AN XY: 74366

African (AFR) AF: 0.484 AC: 20067 AN: 41428

American (AMR) AF: 0.885 AC: 13531 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3361 AN: 3472

East Asian (EAS) AF: 0.867 AC: 4478 AN: 5162

South Asian (SAS) AF: 0.821 AC: 3960 AN: 4824

European-Finnish (FIN) AF: 0.866 AC: 9178 AN: 10594

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.922 AC: 62714 AN: 68022

Other (OTH) AF: 0.808 AC: 1707 AN: 2112

Alfa AF: 0.854 Hom.: 19270

Bravo AF: 0.778

Asia WGS AF: 0.796 AC: 2771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.6
DANN	Benign	0.86
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7098555; hg19: chr10-60592808;