chr9-120903623-T-A

Variant names:

• chr9-120903623-T-A
• rs4836834
• NM_005658.5:c.*1397A>T

Variant summary

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

The NM_005658.5(TRAF1):​c.*1397A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,284 control chromosomes in the GnomAD database, including 18,024 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 0.45 (17988 hom., cov: 32)
  • Exomes 𝑓: 0.52 (36 hom.)
• Consequence: TRAF1 NM_005658.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 21 publications found

Genes affected

TRAF1 (HGNC:12031): (TNF receptor associated factor 1) The protein encoded by this gene is a member of the TNF receptor (TNFR) associated factor (TRAF) protein family. TRAF proteins associate with, and mediate the signal transduction from various receptors of the TNFR superfamily. This protein and TRAF2 form a heterodimeric complex, which is required for TNF-alpha-mediated activation of MAPK8/JNK and NF-kappaB. The protein complex formed by this protein and TRAF2 also interacts with inhibitor-of-apoptosis proteins (IAPs), and thus mediates the anti-apoptotic signals from TNF receptors. The expression of this protein can be induced by Epstein-Barr virus (EBV). EBV infection membrane protein 1 (LMP1) is found to interact with this and other TRAF proteins; this interaction is thought to link LMP1-mediated B lymphocyte transformation to the signal transduction from TNFR family receptors. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

PHF19 (HGNC:24566): (PHD finger protein 19) Enables methylated histone binding activity. Involved in positive regulation of histone H3-K27 methylation. Colocalizes with ESC/E(Z) complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005658.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRAF1	NM_005658.5	MANE Select	c.*1397A>T		3_prime_UTR	Exon 8 of 8	NP_005649.1
	TRAF1	NM_001190945.2		c.*1397A>T		3_prime_UTR	Exon 9 of 9	NP_001177874.1
	TRAF1	NM_001190947.2		c.*1397A>T		3_prime_UTR	Exon 6 of 6	NP_001177876.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRAF1	ENST00000373887.8	TSL:1 MANE Select	c.*1397A>T		3_prime_UTR	Exon 8 of 8	ENSP00000362994.3
	TRAF1	ENST00000540010.1	TSL:1	c.*1397A>T		3_prime_UTR	Exon 9 of 9	ENSP00000443183.1
	TRAF1	ENST00000546084.5	TSL:2	c.*1397A>T		3_prime_UTR	Exon 6 of 6	ENSP00000438583.1

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67932 AN: 151920 Hom.: 17976 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.517

GnomAD4 exome AF: 0.525 AC: 128 AN: 244 Hom.: 36 Cov.: 0 AF XY: 0.543 AC XY: 101 AN XY: 186

African (AFR) AF: 0.00 AC: 0 AN: 8

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.300 AC: 3 AN: 10

South Asian (SAS) AF: 0.833 AC: 5 AN: 6

European-Finnish (FIN) AF: 0.375 AC: 3 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.565 AC: 113 AN: 200

Other (OTH) AF: 0.200 AC: 2 AN: 10

GnomAD4 genome AF: 0.447 AC: 67952 AN: 152040 Hom.: 17988 Cov.: 32 AF XY: 0.454 AC XY: 33706 AN XY: 74320

African (AFR) AF: 0.142 AC: 5877 AN: 41492

American (AMR) AF: 0.562 AC: 8580 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2301 AN: 3472

East Asian (EAS) AF: 0.498 AC: 2569 AN: 5160

South Asian (SAS) AF: 0.692 AC: 3340 AN: 4824

European-Finnish (FIN) AF: 0.542 AC: 5724 AN: 10562

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.558 AC: 37890 AN: 67942

Other (OTH) AF: 0.517 AC: 1093 AN: 2114

Alfa AF: 0.491 Hom.: 2517

Bravo AF: 0.434

Asia WGS AF: 0.559 AC: 1941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.34
DANN	Benign	0.67
PhyloP100		-1.4
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: rs4836834; hg19: chr9-123665901;