18-56261410-A-G

Variant names:

• chr18-56261410-A-G
• rs2538026
• ENST00000745030.1:n.645+450A>G

Variant summary

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

The ENST00000745030.1(ENSG00000297056):​n.645+450A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,098 control chromosomes in the GnomAD database, including 47,351 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 0.78 (47351 hom., cov: 32)
• Consequence: ENSG00000297056 ENST00000745030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 2 publications found

Genes affected

ENSG00000297056 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297056	ENST00000745030.1	n.645+450A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119067 AN: 151980 Hom.: 47290 Cov.: 32

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.784 AC: 119192 AN: 152098 Hom.: 47351 Cov.: 32 AF XY: 0.782 AC XY: 58114 AN XY: 74334

African (AFR) AF: 0.906 AC: 37613 AN: 41516

American (AMR) AF: 0.784 AC: 11967 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2611 AN: 3470

East Asian (EAS) AF: 0.929 AC: 4814 AN: 5180

South Asian (SAS) AF: 0.642 AC: 3090 AN: 4812

European-Finnish (FIN) AF: 0.699 AC: 7378 AN: 10550

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.724 AC: 49206 AN: 67990

Other (OTH) AF: 0.777 AC: 1642 AN: 2112

Alfa AF: 0.764 Hom.: 16724

Bravo AF: 0.798

Asia WGS AF: 0.797 AC: 2771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.59
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2538026; hg19: chr18-53928641;