18-78927314-G-A

Position:

• chr18-78927314-G-A

Variant summary

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

The ENST00000580639.1(ENSG00000265101):​n.128C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,228 control chromosomes in the GnomAD database, including 22,034 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 0.53 (22026 hom., cov: 35)
  • Exomes 𝑓: 0.79 (8 hom.)
• Consequence: ENST00000580639.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372224	XR_935678.3	n.60C>T		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000580639.1	n.128C>T		non_coding_transcript_exon_variant	1/2	3
	ENST00000654461.1	n.437+11G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80485 AN: 152082 Hom.: 22024 Cov.: 35

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.550

GnomAD4 exome AF: 0.786 AC: 22 AN: 28 Hom.: 8 Cov.: 0 AF XY: 0.875 AC XY: 14 AN XY: 16

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.800

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.529 AC: 80515 AN: 152200 Hom.: 22026 Cov.: 35 AF XY: 0.525 AC XY: 39100 AN XY: 74416

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.553

Alfa AF: 0.600 Hom.: 55893

Bravo AF: 0.519

Asia WGS AF: 0.442 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs936503; hg19: chr18-76687314;