chr18-6728489-G-A

Position:

• chr18-6728489-G-A

Variant summary

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

The ENST00000623844.1(ENSG00000279479):​n.1437G>A 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 0.533 in 152,072 control chromosomes in the GnomAD database, including 21,864 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 (21864 hom., cov: 33)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: ENSG00000279479 ENST00000623844.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

Genes affected

ENSG00000279479 (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 (SAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.6728489G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000279479	ENST00000623844.1	n.1437G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.533 AC: 81027 AN: 151948 Hom.: 21822 Cov.: 33

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.532

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.333

GnomAD4 genome AF: 0.533 AC: 81124 AN: 152066 Hom.: 21864 Cov.: 33 AF XY: 0.536 AC XY: 39849 AN XY: 74332

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.530

Alfa AF: 0.533 Hom.: 3656

Bravo AF: 0.534

Asia WGS AF: 0.583 AC: 2029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.32
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7233739; hg19: chr18-6728488;