5-176707401-C-T

Position:

• chr5-176707401-C-T

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/exons	MANE	Protein	UniProt
		n.176707401C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000248484	ENST00000507236.1	n.533G>A		non_coding_transcript_exon_variant	2/2	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;