2-238320563-GC-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015650.4(TRAF3IP1):c.-99del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 980,564 control chromosomes in the GnomAD database, including 3,436 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.062 (395 hom., cov: 32)
  • Exomes 𝑓: 0.086 (3041 hom.)
• Consequence: TRAF3IP1 NM_015650.4 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.166

Genes affected

TRAF3IP1 (HGNC:17861): (TRAF3 interacting protein 1) The protein encoded by this gene interacts with TNF receptor-associated factor 3, tethering it to cytoskeletal microtubules. The encoded protein is also an inhibitor of the innate type I IFN response. Defects in this gene are a cause of Senior-Loken syndrome 9. [provided by RefSeq, Mar 2017]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 2-238320563-GC-G is Benign according to our data. Variant chr2-238320563-GC-G is described in ClinVar as [Benign]. Clinvar id is 1281208.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.091 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAF3IP1	NM_015650.4	c.-99del		5_prime_UTR_variant	1/17	ENST00000373327.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAF3IP1	ENST00000373327.5	c.-99del		5_prime_UTR_variant	1/17	1	NM_015650.4
TRAF3IP1	ENST00000391993.7	c.-99del		5_prime_UTR_variant	1/15	1		P1
TRAF3IP1	ENST00000409739.2	c.-99del		5_prime_UTR_variant, NMD_transcript_variant	1/5	3

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 9340 AN: 150644 Hom.: 396 Cov.: 32

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0379

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.0551

GnomAD4 exome AF: 0.0857 AC: 71088 AN: 829816 Hom.: 3041 Cov.: 11 AF XY: 0.0865 AC XY: 33648 AN XY: 389146

Gnomad4 AFR exome AF: 0.00939

Gnomad4 AMR exome AF: 0.0503

Gnomad4 ASJ exome AF: 0.149

Gnomad4 EAS exome AF: 0.000992

Gnomad4 SAS exome AF: 0.0578

Gnomad4 FIN exome AF: 0.162

Gnomad4 NFE exome AF: 0.0873

Gnomad4 OTH exome AF: 0.0881

GnomAD4 genome AF: 0.0619 AC: 9332 AN: 150748 Hom.: 395 Cov.: 32 AF XY: 0.0597 AC XY: 4399 AN XY: 73658

Gnomad4 AFR AF: 0.0144

Gnomad4 AMR AF: 0.0378

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0514

Gnomad4 FIN AF: 0.0920

Gnomad4 NFE AF: 0.0929

Gnomad4 OTH AF: 0.0540

Alfa AF: 0.0444 Hom.: 62

Bravo AF: 0.0543

Asia WGS AF: 0.0290 AC: 95 AN: 3306

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 14, 2020

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Computational scores

Source: dbNSFP v4.3

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: rs368022925; hg19: chr2-239229204;