18-49643445-A-T

Variant names:

• chr18-49643445-A-T
• rs1943981
• ENST00000849192.1:n.232-13442A>T

Variant summary

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

The ENST00000849192.1(ENSG00000310339):​n.232-13442A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 128,974 control chromosomes in the GnomAD database, including 31,379 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 0.73 (31379 hom., cov: 28)
• Consequence: ENSG00000310339 ENST00000849192.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 7 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849192.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310339	ENST00000849192.1		n.232-13442A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.733 AC: 94410 AN: 128850 Hom.: 31333 Cov.: 28

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.733 AC: 94517 AN: 128974 Hom.: 31379 Cov.: 28 AF XY: 0.732 AC XY: 45979 AN XY: 62852

African (AFR) AF: 0.878 AC: 35595 AN: 40562

American (AMR) AF: 0.723 AC: 9560 AN: 13224

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 1816 AN: 2684

East Asian (EAS) AF: 0.628 AC: 2320 AN: 3694

South Asian (SAS) AF: 0.685 AC: 2726 AN: 3978

European-Finnish (FIN) AF: 0.667 AC: 5567 AN: 8346

Middle Eastern (MID) AF: 0.648 AC: 158 AN: 244

European-Non Finnish (NFE) AF: 0.653 AC: 35214 AN: 53914

Other (OTH) AF: 0.698 AC: 1247 AN: 1786

Alfa AF: 0.112 Hom.: 137

Bravo AF: 0.642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.73
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs1943981; hg19: chr18-47169815;