18-55750408-A-G

Position:

• chr18-55750408-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000587346.1(ENSG00000267284):​n.140-10895A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.858 in 152,178 control chromosomes in the GnomAD database, including 56,085 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 0.86 (56085 hom., cov: 32)
• Consequence: ENSG00000267284 ENST00000587346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372130	XR_007066382.1	n.329-34491A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267284	ENST00000587346.1	n.140-10895A>G		intron_variant		4
ENSG00000267284	ENST00000589662.1	n.217+28874A>G		intron_variant		5
ENSG00000267284	ENST00000592936.1	n.473-8632A>G		intron_variant		4
ENSG00000267284	ENST00000654829.1	n.157-34491A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.858 AC: 130475 AN: 152060 Hom.: 56040 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.858 AC: 130574 AN: 152178 Hom.: 56085 Cov.: 32 AF XY: 0.860 AC XY: 64005 AN XY: 74390

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.909

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.788

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.876

Alfa AF: 0.847 Hom.: 6748

Bravo AF: 0.866

Asia WGS AF: 0.908 AC: 3155 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs796743; hg19: chr18-53417639;