18-895115-C-T

Position:

• chr18-895115-C-T

Variant summary

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

The ENST00000582554.1(ENSG00000265671):​n.91-420G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,066 control chromosomes in the GnomAD database, including 31,153 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 0.62 (31153 hom., cov: 34)
• Consequence: ENSG00000265671 ENST00000582554.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

Genes affected

ENSG00000265671 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000265671	ENST00000582554.1	n.91-420G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94049 AN: 151948 Hom.: 31150 Cov.: 34

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.619 AC: 94080 AN: 152066 Hom.: 31153 Cov.: 34 AF XY: 0.622 AC XY: 46214 AN XY: 74338

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.651

Alfa AF: 0.660 Hom.: 4292

Bravo AF: 0.610

Asia WGS AF: 0.732 AC: 2529 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4798684; hg19: chr18-895116;