18-73923401-T-G

Variant names:

• chr18-73923401-T-G
• rs12454898
• ENST00000581541.1:n.122-8372A>C

Variant summary

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

The ENST00000581541.1(ENSG00000263655):​n.122-8372A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,046 control chromosomes in the GnomAD database, including 9,621 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 0.33 (9621 hom., cov: 32)
• Consequence: ENSG00000263655 ENST00000581541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390
• Publications: 1 publications found

Genes affected

ENSG00000263655 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.507 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
ENSG00000263655	ENST00000581541.1	n.122-8372A>C		intron_variant	Intron 1 of 2	3
ENSG00000263655	ENST00000753906.1	n.180-8372A>C		intron_variant	Intron 2 of 3
ENSG00000263655	ENST00000753907.1	n.191-8372A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49721 AN: 151928 Hom.: 9605 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.327 AC: 49748 AN: 152046 Hom.: 9621 Cov.: 32 AF XY: 0.331 AC XY: 24637 AN XY: 74320

African (AFR) AF: 0.142 AC: 5888 AN: 41492

American (AMR) AF: 0.517 AC: 7892 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1341 AN: 3464

East Asian (EAS) AF: 0.173 AC: 895 AN: 5174

South Asian (SAS) AF: 0.380 AC: 1829 AN: 4818

European-Finnish (FIN) AF: 0.387 AC: 4080 AN: 10546

Middle Eastern (MID) AF: 0.397 AC: 115 AN: 290

European-Non Finnish (NFE) AF: 0.392 AC: 26613 AN: 67974

Other (OTH) AF: 0.325 AC: 685 AN: 2108

Alfa AF: 0.376 Hom.: 20756

Bravo AF: 0.330

Asia WGS AF: 0.280 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.070
DANN	Benign	0.59
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs12454898; hg19: chr18-71590636;