NM_015650.4:c.885G>T
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_015650.4(TRAF3IP1):c.885G>T(p.Lys295Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 1,409,052 control chromosomes in the GnomAD database, including 63,095 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. K295K) has been classified as Likely benign.
Frequency
Consequence
NM_015650.4 missense
Scores
Clinical Significance
Conservation
Publications
- Senior-Loken syndrome 9Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- Senior-Loken syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- short rib-polydactyly syndrome, Majewski typeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRAF3IP1 | ENST00000373327.5 | c.885G>T | p.Lys295Asn | missense_variant | Exon 5 of 17 | 1 | NM_015650.4 | ENSP00000362424.4 | ||
TRAF3IP1 | ENST00000391993.7 | c.885G>T | p.Lys295Asn | missense_variant | Exon 5 of 15 | 1 | ENSP00000375851.3 | |||
TRAF3IP1 | ENST00000409739.2 | n.*754G>T | non_coding_transcript_exon_variant | Exon 5 of 5 | 3 | ENSP00000386648.2 | ||||
TRAF3IP1 | ENST00000409739.2 | n.*754G>T | 3_prime_UTR_variant | Exon 5 of 5 | 3 | ENSP00000386648.2 |
Frequencies
GnomAD3 genomes AF: 0.243 AC: 36867AN: 151992Hom.: 5437 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.289 AC: 42716AN: 147800 AF XY: 0.294 show subpopulations
GnomAD4 exome AF: 0.299 AC: 375680AN: 1256942Hom.: 57660 Cov.: 36 AF XY: 0.300 AC XY: 182204AN XY: 607906 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.242 AC: 36861AN: 152110Hom.: 5435 Cov.: 31 AF XY: 0.240 AC XY: 17869AN XY: 74346 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:3
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at