ENST00000789038.1:n.87-32426G>A

Variant names:

• chr10-83752139-C-T
• rs11200394
• ENST00000789038.1:n.87-32426G>A

Variant summary

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

The ENST00000789038.1(ENSG00000286876):​n.87-32426G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0775 in 152,222 control chromosomes in the GnomAD database, including 567 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 0.077 (567 hom., cov: 33)
• Consequence: ENSG00000286876 ENST00000789038.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 2 publications found

Genes affected

ENSG00000286876 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789038.1. 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
	ENSG00000286876	ENST00000789038.1		n.87-32426G>A		intron	N/A
	ENSG00000286876	ENST00000789039.1		n.282+21767G>A		intron	N/A
	ENSG00000286876	ENST00000789040.1		n.54+7408G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0775 AC: 11781 AN: 152104 Hom.: 568 Cov.: 33

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.0573

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0982

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0775 AC: 11792 AN: 152222 Hom.: 567 Cov.: 33 AF XY: 0.0784 AC XY: 5832 AN XY: 74416

African (AFR) AF: 0.0258 AC: 1072 AN: 41552

American (AMR) AF: 0.0572 AC: 875 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3470

East Asian (EAS) AF: 0.106 AC: 549 AN: 5170

South Asian (SAS) AF: 0.149 AC: 719 AN: 4828

European-Finnish (FIN) AF: 0.0939 AC: 995 AN: 10594

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0982 AC: 6680 AN: 68000

Other (OTH) AF: 0.0601 AC: 127 AN: 2112

Alfa AF: 0.0452 Hom.: 60

Bravo AF: 0.0704

Asia WGS AF: 0.0990 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.0
DANN	Benign	0.27
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs11200394; hg19: chr10-85511895;