ENST00000834100.1:n.365-16555A>G

Variant names:

• chr7-94250781-T-C
• rs2110483
• ENST00000834100.1:n.365-16555A>G

Variant summary

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

The ENST00000834100.1(ENSG00000285090):​n.365-16555A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 151,956 control chromosomes in the GnomAD database, including 4,592 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 0.18 (4592 hom., cov: 32)
• Consequence: ENSG00000285090 ENST00000834100.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 1 publications found

Genes affected

ENSG00000285090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834100.1. 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
	ENSG00000285090	ENST00000834100.1		n.365-16555A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26929 AN: 151838 Hom.: 4573 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.0870

Gnomad EAS AF: 0.0455

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.0270

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.0637

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.178 AC: 26994 AN: 151956 Hom.: 4592 Cov.: 32 AF XY: 0.172 AC XY: 12748 AN XY: 74272

African (AFR) AF: 0.451 AC: 18641 AN: 41364

American (AMR) AF: 0.155 AC: 2358 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0870 AC: 301 AN: 3460

East Asian (EAS) AF: 0.0455 AC: 235 AN: 5170

South Asian (SAS) AF: 0.0726 AC: 350 AN: 4822

European-Finnish (FIN) AF: 0.0270 AC: 286 AN: 10594

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.0637 AC: 4333 AN: 67974

Other (OTH) AF: 0.163 AC: 343 AN: 2110

Alfa AF: 0.130 Hom.: 1078

Bravo AF: 0.202

Asia WGS AF: 0.0970 AC: 339 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.55
DANN	Benign	0.45
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2110483; hg19: chr7-93880093;