rs57302454

Variant names:

• chr8-23081148-G-C
• rs57302454
• ENST00000501897.1:n.264+92G>C

Variant summary

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

The ENST00000501897.1(TNFRSF10B-AS1):​n.264+92G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0778 in 332,230 control chromosomes in the GnomAD database, including 1,950 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 0.10 (1539 hom., cov: 32)
  • Exomes 𝑓: 0.056 (411 hom.)
• Consequence: TNFRSF10B-AS1 ENST00000501897.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.962
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000501897.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFRSF10B-AS1	NR_038873.1		n.264+92G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFRSF10B-AS1	ENST00000501897.1	TSL:2	n.264+92G>C		intron	N/A
	TNFRSF10B-AS1	ENST00000809992.1		n.126+92G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15781 AN: 152068 Hom.: 1538 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0550

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.0581

Gnomad SAS AF: 0.0824

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0402

Gnomad OTH AF: 0.0809

GnomAD4 exome AF: 0.0558 AC: 10049 AN: 180044 Hom.: 411 Cov.: 0 AF XY: 0.0569 AC XY: 5855 AN XY: 102838

African (AFR) AF: 0.273 AC: 1147 AN: 4194

American (AMR) AF: 0.0316 AC: 442 AN: 14006

Ashkenazi Jewish (ASJ) AF: 0.0436 AC: 142 AN: 3256

East Asian (EAS) AF: 0.0673 AC: 499 AN: 7420

South Asian (SAS) AF: 0.0849 AC: 2225 AN: 26220

European-Finnish (FIN) AF: 0.0405 AC: 700 AN: 17282

Middle Eastern (MID) AF: 0.0489 AC: 104 AN: 2126

European-Non Finnish (NFE) AF: 0.0446 AC: 4332 AN: 97096

Other (OTH) AF: 0.0542 AC: 458 AN: 8444

GnomAD4 genome AF: 0.104 AC: 15802 AN: 152186 Hom.: 1539 Cov.: 32 AF XY: 0.102 AC XY: 7570 AN XY: 74418

African (AFR) AF: 0.261 AC: 10830 AN: 41494

American (AMR) AF: 0.0549 AC: 840 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 165 AN: 3470

East Asian (EAS) AF: 0.0580 AC: 301 AN: 5188

South Asian (SAS) AF: 0.0828 AC: 399 AN: 4816

European-Finnish (FIN) AF: 0.0317 AC: 336 AN: 10602

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0401 AC: 2730 AN: 67998

Other (OTH) AF: 0.0801 AC: 169 AN: 2110

Alfa AF: 0.0760 Hom.: 129

Bravo AF: 0.111

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.18
DANN	Benign	0.65
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs57302454; hg19: chr8-22938661; COSMIC: COSV67166642;