ENST00000844037.1:n.162+10046A>G

Variant names:

• chr18-77240802-T-C
• rs8084125
• ENST00000844037.1:n.162+10046A>G

Variant summary

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

The ENST00000844037.1(ENSG00000309801):​n.162+10046A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,246 control chromosomes in the GnomAD database, including 1,567 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 0.14 (1567 hom., cov: 32)
• Consequence: ENSG00000309801 ENST00000844037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 7 publications found

Genes affected

ENSG00000309801 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844037.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309801	ENST00000844037.1		n.162+10046A>G		intron	N/A
	ENSG00000309801	ENST00000844038.1		n.118+9999A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20715 AN: 152128 Hom.: 1570 Cov.: 32

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.136 AC: 20714 AN: 152246 Hom.: 1567 Cov.: 32 AF XY: 0.137 AC XY: 10191 AN XY: 74416

African (AFR) AF: 0.0926 AC: 3846 AN: 41550

American (AMR) AF: 0.118 AC: 1803 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5182

South Asian (SAS) AF: 0.176 AC: 851 AN: 4832

European-Finnish (FIN) AF: 0.193 AC: 2041 AN: 10576

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11153 AN: 68012

Other (OTH) AF: 0.135 AC: 285 AN: 2110

Alfa AF: 0.152 Hom.: 3475

Bravo AF: 0.128

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.5
DANN	Benign	0.41
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs8084125; hg19: chr18-74952758;