18-73923401-T-G

Position:

• chr18-73923401-T-G

Variant summary

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

The ENST00000581541.1(ENSG00000263655):​n.122-8372A>C variant causes a intron, non coding transcript 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: ENST00000581541.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390

Genes affected

(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 (AMR) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000581541.1	n.122-8372A>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.325

Alfa AF: 0.383 Hom.: 15259

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12454898; hg19: chr18-71590636;