chr13-23614884-C-T

Position:

• chr13-23614884-C-T

Variant summary

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

The NM_148957.4(TNFRSF19):​c.181-983C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,222 control chromosomes in the GnomAD database, including 21,085 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 (21085 hom., cov: 29)
• Consequence: TNFRSF19 NM_148957.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

Genes affected

TNFRSF19 (HGNC:11915): (TNF receptor superfamily member 19) The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor is highly expressed during embryonic development. It has been shown to interact with TRAF family members, and to activate JNK signaling pathway when overexpressed in cells. This receptor is capable of inducing apoptosis by a caspase-independent mechanism, and it is thought to play an essential role in embryonic development. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNFRSF19	NM_148957.4	c.181-983C>T		intron_variant		ENST00000248484.9	NP_683760.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNFRSF19	ENST00000248484.9	c.181-983C>T		intron_variant		1	NM_148957.4	ENSP00000248484	P1
TNFRSF19	ENST00000382258.8	c.181-983C>T		intron_variant		1		ENSP00000371693
TNFRSF19	ENST00000382263.3	c.181-983C>T		intron_variant		1		ENSP00000371698	P1
TNFRSF19	ENST00000403372.6	c.-216-983C>T		intron_variant		2		ENSP00000385408

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78025 AN: 151110 Hom.: 21080 Cov.: 29

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.516 AC: 78050 AN: 151222 Hom.: 21085 Cov.: 29 AF XY: 0.514 AC XY: 37960 AN XY: 73838

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.518

Alfa AF: 0.546 Hom.: 4084

Bravo AF: 0.502

Asia WGS AF: 0.542 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.6
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9317882; hg19: chr13-24189023;