ENST00000501897.1:n.193-642G>A

Variant names:

• chr8-23080343-G-A
• rs4268128
• ENST00000501897.1:n.193-642G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000501897.1(TNFRSF10B-AS1):​n.193-642G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.839 in 152,166 control chromosomes in the GnomAD database, including 53,931 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 0.84 (53931 hom., cov: 31)
• Consequence: TNFRSF10B-AS1 ENST00000501897.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899
• Publications: 19 publications found

Genes affected

TNFRSF10B-AS1 (HGNC:27809):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFRSF10B-AS1	NR_038873.1	n.193-642G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFRSF10B-AS1	ENST00000501897.1	n.193-642G>A		intron_variant	Intron 1 of 2	2
TNFRSF10B-AS1	ENST00000809992.1	n.55-642G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127588 AN: 152048 Hom.: 53881 Cov.: 31

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.837

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.839 AC: 127696 AN: 152166 Hom.: 53931 Cov.: 31 AF XY: 0.840 AC XY: 62491 AN XY: 74392

African (AFR) AF: 0.921 AC: 38245 AN: 41530

American (AMR) AF: 0.869 AC: 13290 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2551 AN: 3472

East Asian (EAS) AF: 0.823 AC: 4258 AN: 5174

South Asian (SAS) AF: 0.891 AC: 4300 AN: 4828

European-Finnish (FIN) AF: 0.770 AC: 8142 AN: 10574

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54121 AN: 67974

Other (OTH) AF: 0.838 AC: 1773 AN: 2116

Alfa AF: 0.817 Hom.: 39170

Bravo AF: 0.852

Asia WGS AF: 0.879 AC: 3060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.62
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs4268128; hg19: chr8-22937856;