18-60427176-A-G

Position:

• chr18-60427176-A-G

Variant summary

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

The ENST00000658928.1(ENSG00000285681):​n.157-52395A>G 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 0.579 in 151,704 control chromosomes in the GnomAD database, including 25,667 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 0.58 (25667 hom., cov: 32)
• Consequence: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.943

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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
	ENST00000658928.1	n.157-52395A>G		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.114-52395A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87871 AN: 151586 Hom.: 25663 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.579 AC: 87911 AN: 151704 Hom.: 25667 Cov.: 32 AF XY: 0.581 AC XY: 43043 AN XY: 74116

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.563

Alfa AF: 0.581 Hom.: 3282

Bravo AF: 0.576

Asia WGS AF: 0.613 AC: 2131 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1943232; hg19: chr18-58094409;