ENST00000507236.1:n.533G>A

Variant names:

• chr5-176707401-C-T
• rs4868699
• ENST00000507236.1:n.533G>A

Variant summary

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

The ENST00000507236.1(ENSG00000248484):​n.533G>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 0.883 in 152,292 control chromosomes in the GnomAD database, including 59,545 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 0.88 (59542 hom., cov: 33)
  • Exomes 𝑓: 0.88 (3 hom.)
• Consequence: ENSG00000248484 ENST00000507236.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759

Genes affected

ENSG00000248484 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 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
ENSG00000248484	ENST00000507236.1	n.533G>A		non_coding_transcript_exon_variant	Exon 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134439 AN: 152166 Hom.: 59503 Cov.: 33

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.874

GnomAD4 exome AF: 0.875 AC: 7 AN: 8 Hom.: 3 Cov.: 0 AF XY: 0.833 AC XY: 5 AN XY: 6

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.883 AC: 134532 AN: 152284 Hom.: 59542 Cov.: 33 AF XY: 0.880 AC XY: 65482 AN XY: 74452

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.834

Gnomad4 FIN AF: 0.894

Gnomad4 NFE AF: 0.890

Gnomad4 OTH AF: 0.868

Alfa AF: 0.880 Hom.: 21409

Bravo AF: 0.879

Asia WGS AF: 0.825 AC: 2865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4868699; hg19: chr5-176134402;