13-23614884-C-T

Variant names:

• chr13-23614884-C-T
• rs9317882
• NM_148957.4:c.181-983C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TNFRSF19	NM_148957.4	c.181-983C>T		intron_variant	Intron 3 of 9	ENST00000248484.9	NP_683760.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFRSF19	ENST00000248484.9	c.181-983C>T		intron_variant	Intron 3 of 9	1	NM_148957.4	ENSP00000248484.4
TNFRSF19	ENST00000382258.8	c.181-983C>T		intron_variant	Intron 3 of 8	1		ENSP00000371693.4
TNFRSF19	ENST00000382263.3	c.181-983C>T		intron_variant	Intron 3 of 9	1		ENSP00000371698.3
TNFRSF19	ENST00000403372.6	c.-216-983C>T		intron_variant	Intron 1 of 7	2		ENSP00000385408.2

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

African (AFR) AF: 0.365 AC: 15045 AN: 41192

American (AMR) AF: 0.476 AC: 7234 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1832 AN: 3458

East Asian (EAS) AF: 0.528 AC: 2720 AN: 5152

South Asian (SAS) AF: 0.564 AC: 2698 AN: 4782

European-Finnish (FIN) AF: 0.549 AC: 5686 AN: 10364

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.604 AC: 40922 AN: 67782

Other (OTH) AF: 0.518 AC: 1084 AN: 2094

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
PhyloP100		0.080
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9317882; hg19: chr13-24189023;