18-51022369-A-T

Position:

• chr18-51022369-A-T

Variant summary

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

The ENST00000590722.2(ENSG00000267699):​n.158-24551A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.965 in 152,304 control chromosomes in the GnomAD database, including 70,935 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 0.96 (70935 hom., cov: 31)
• Consequence: ENSG00000267699 ENST00000590722.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

Genes affected

ENSG00000267699 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985152	XR_007066370.1	n.177+7549T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267699	ENST00000590722.2	n.158-24551A>T		intron_variant		2		ENSP00000465737.1
ENSG00000267699	ENST00000588256.1	n.335-24551A>T		intron_variant		4
ENSG00000289868	ENST00000701227.1	n.134-2744T>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.965 AC: 146810 AN: 152186 Hom.: 70877 Cov.: 31

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.974

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

GnomAD4 genome AF: 0.965 AC: 146927 AN: 152304 Hom.: 70935 Cov.: 31 AF XY: 0.964 AC XY: 71804 AN XY: 74470

Gnomad4 AFR AF: 0.991

Gnomad4 AMR AF: 0.974

Gnomad4 ASJ AF: 0.967

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.937

Gnomad4 FIN AF: 0.937

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.975

Alfa AF: 0.955 Hom.: 8623

Bravo AF: 0.971

Asia WGS AF: 0.975 AC: 3388 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	0.36
DANN	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1787111; hg19: chr18-48548739;