8-24912339-A-G

Variant names:

• chr8-24912339-A-G
• rs1457266
• ENST00000607058.2:n.2379T>C

Variant summary

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

The ENST00000607058.2(ENSG00000272163):​n.2379T>C 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 0.524 in 152,064 control chromosomes in the GnomAD database, including 24,095 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 0.52 (24095 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000272163 ENST00000607058.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

Genes affected

ENSG00000272163 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.673 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
ENSG00000272163	ENST00000607058.2	n.2379T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79695 AN: 151946 Hom.: 24083 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.524

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.524 AC: 79717 AN: 152064 Hom.: 24095 Cov.: 32 AF XY: 0.531 AC XY: 39437 AN XY: 74328

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.526

Alfa AF: 0.616 Hom.: 27525

Bravo AF: 0.515

Asia WGS AF: 0.630 AC: 2188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.5
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1457266; hg19: chr8-24769852;