8-24912339-A-G

Position:

• chr8-24912339-A-G

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: ENST00000607058.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000607058.2	n.2379T>C		non_coding_transcript_exon_variant	1/1

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;