3-49853180-C-T

Position:

• chr3-49853180-C-T

Variant summary

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

The NM_005879.3(TRAIP):​c.98+3176G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,424 control chromosomes in the GnomAD database, including 16,647 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 0.46 (16647 hom., cov: 32)
• Consequence: TRAIP NM_005879.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

TRAIP (HGNC:30764): (TRAF interacting protein) This gene encodes a protein that contains an N-terminal RING finger motif and a putative coiled-coil domain. A similar murine protein interacts with TNFR-associated factor 1 (TRAF1), TNFR-associated factor 2 (TRAF2), and cylindromatosis. The interaction with TRAF2 inhibits TRAF2-mediated nuclear factor kappa-B, subunit 1 activation that is required for cell activation and protection against apoptosis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRAIP	NM_005879.3	c.98+3176G>A		intron_variant		ENST00000331456.7	NP_005870.2
TRAIP	XM_017005526.2	c.98+3176G>A		intron_variant			XP_016861015.1
TRAIP	XR_007094382.1	n.209+3176G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRAIP	ENST00000331456.7	c.98+3176G>A		intron_variant		1	NM_005879.3	ENSP00000328203	P1

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69479 AN: 151320 Hom.: 16624 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.459 AC: 69541 AN: 151424 Hom.: 16647 Cov.: 32 AF XY: 0.449 AC XY: 33177 AN XY: 73930

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.465

Alfa AF: 0.469 Hom.: 3589

Bravo AF: 0.466

Asia WGS AF: 0.365 AC: 1268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.75
DANN	Benign	0.25

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: rs2352974; hg19: chr3-49890613;