18-2825420-T-G

Variant names:

• chr18-2825420-T-G
• rs673783
• ENST00000581172.1:n.451-2849A>C

Variant summary

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

The ENST00000581172.1(ENSG00000266049):​n.451-2849A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,136 control chromosomes in the GnomAD database, including 6,140 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 0.26 (6140 hom., cov: 32)
• Consequence: ENSG00000266049 ENST00000581172.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 9 publications found

Genes affected

ENSG00000266049 (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 (NFE) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000581172.1. 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
	ENSG00000266049	ENST00000581172.1	TSL:3	n.451-2849A>C		intron	N/A
	ENSG00000266049	ENST00000583546.1	TSL:3	n.308+7196A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39623 AN: 152018 Hom.: 6138 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.261 AC: 39639 AN: 152136 Hom.: 6140 Cov.: 32 AF XY: 0.258 AC XY: 19169 AN XY: 74378

African (AFR) AF: 0.104 AC: 4302 AN: 41526

American (AMR) AF: 0.312 AC: 4768 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 899 AN: 3468

East Asian (EAS) AF: 0.136 AC: 704 AN: 5188

South Asian (SAS) AF: 0.170 AC: 816 AN: 4808

European-Finnish (FIN) AF: 0.329 AC: 3478 AN: 10572

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23816 AN: 67980

Other (OTH) AF: 0.262 AC: 552 AN: 2108

Alfa AF: 0.306 Hom.: 21022

Bravo AF: 0.246

Asia WGS AF: 0.158 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.47
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs673783; hg19: chr18-2825418;