18-73914271-T-G

Variant names:

• chr18-73914271-T-G
• rs2278331
• ENST00000581541.1:n.*134A>C

Variant summary

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

The ENST00000581541.1(ENSG00000263655):​n.*134A>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,960 control chromosomes in the GnomAD database, including 8,695 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 (8695 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000263655 ENST00000581541.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.644

Genes affected

ENSG00000263655 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 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.*134A>C		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49878 AN: 151842 Hom.: 8689 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.329

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.328 AC: 49912 AN: 151960 Hom.: 8695 Cov.: 31 AF XY: 0.332 AC XY: 24671 AN XY: 74270

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.330

Alfa AF: 0.300 Hom.: 2720

Bravo AF: 0.316

Asia WGS AF: 0.541 AC: 1880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2278331; hg19: chr18-71581506;