8-23225458-G-T

Position:

• chr8-23225458-G-T

Variant summary

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

The ENST00000511929.2(ENSG00000250714):​n.914-14C>A variant causes a splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 142,172 control chromosomes in the GnomAD database, including 14,422 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency:
  • Genomes: 𝑓 0.42 (14422 hom., cov: 21)
  • Exomes 𝑓: 0.20 (339 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000511929.2 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -1.75

Genes affected

TNFRSF10A-DT (HGNC:52647): (TNFRSF10A divergent transcript)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFRSF10A-DT	NR_033928.1	n.238G>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFRSF10A-DT	ENST00000500853.1	n.238G>T		non_coding_transcript_exon_variant	1/3	2
	ENST00000511929.2	n.914-14C>A		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		3
TNFRSF10A-DT	ENST00000517774.1	n.422-347G>T		intron_variant, non_coding_transcript_variant		4
TNFRSF10A-DT	ENST00000670072.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.417 AC: 59193 AN: 142070 Hom.: 14419 Cov.: 21

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.507

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.437

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.199 AC: 1359 AN: 6814 Hom.: 339 Cov.: 0 AF XY: 0.206 AC XY: 725 AN XY: 3524

Gnomad4 AFR exome AF: 0.0620

Gnomad4 AMR exome AF: 0.278

Gnomad4 ASJ exome AF: 0.389

Gnomad4 EAS exome AF: 0.0801

Gnomad4 SAS exome AF: 0.523

Gnomad4 FIN exome AF: 0.220

Gnomad4 NFE exome AF: 0.212

Gnomad4 OTH exome AF: 0.188

GnomAD4 genome AF: 0.416 AC: 59205 AN: 142172 Hom.: 14422 Cov.: 21 AF XY: 0.419 AC XY: 28595 AN XY: 68316

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.658

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.433

Alfa AF: 0.496 Hom.: 10127

Bravo AF: 0.415

Asia WGS AF: 0.465 AC: 1620 AN: 3478

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

not provided, no classification provided

not provided

Department of Ophthalmology and Visual Sciences Kyoto University

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13278062; hg19: chr8-23082971;