ENST00000849189.1:n.359-2463G>T

Variant names:

• chr18-49697541-G-T
• rs1943984
• ENST00000849189.1:n.359-2463G>T

Variant summary

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

The ENST00000849189.1(ENSG00000310339):​n.359-2463G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,088 control chromosomes in the GnomAD database, including 4,285 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 (4285 hom., cov: 32)
• Consequence: ENSG00000310339 ENST00000849189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 1 publications found

Genes affected

ENSG00000310339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372112	XR_007066363.1	n.289-2463G>T		intron_variant	Intron 2 of 4
LOC105372112	XR_007066364.1	n.534-2463G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310339	ENST00000849189.1	n.359-2463G>T		intron_variant	Intron 2 of 3
ENSG00000310339	ENST00000849190.1	n.-115G>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28069 AN: 151970 Hom.: 4278 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0871

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0650

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.185 AC: 28122 AN: 152088 Hom.: 4285 Cov.: 32 AF XY: 0.186 AC XY: 13859 AN XY: 74346

African (AFR) AF: 0.405 AC: 16805 AN: 41454

American (AMR) AF: 0.190 AC: 2896 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0556 AC: 193 AN: 3472

East Asian (EAS) AF: 0.374 AC: 1926 AN: 5150

South Asian (SAS) AF: 0.120 AC: 578 AN: 4822

European-Finnish (FIN) AF: 0.0871 AC: 923 AN: 10594

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0650 AC: 4423 AN: 68006

Other (OTH) AF: 0.143 AC: 301 AN: 2110

Alfa AF: 0.0732 Hom.: 334

Bravo AF: 0.219

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.58
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1943984; hg19: chr18-47223911;