rs7233739

Variant names:

• chr18-6728489-G-A
• rs7233739
• ENST00000623844.1:n.1437G>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279479	ENST00000623844.1	n.1437G>A		non_coding_transcript_exon_variant	Exon 1 of 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;