rs1323855

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000299413.7(TRIM44):​c.1007+11165C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0148 in 152,020 control chromosomes in the GnomAD database, including 56 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 0.015 ( 56 hom., cov: 31)

Consequence

TRIM44
ENST00000299413.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.151
Variant links:
Genes affected
TRIM44 (HGNC:19016): (tripartite motif containing 44) This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, namely a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0148 (2246/152020) while in subpopulation AFR AF= 0.051 (2114/41466). AF 95% confidence interval is 0.0492. There are 56 homozygotes in gnomad4. There are 1056 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2246 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRIM44NM_017583.6 linkuse as main transcriptc.1007+11165C>T intron_variant ENST00000299413.7 NP_060053.2
TRIM44XM_006718254.2 linkuse as main transcriptc.767+11165C>T intron_variant XP_006718317.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TRIM44ENST00000299413.7 linkuse as main transcriptc.1007+11165C>T intron_variant 1 NM_017583.6 ENSP00000299413 P1
TRIM44ENST00000532066.1 linkuse as main transcriptn.373+11165C>T intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.0148
AC:
2241
AN:
151906
Hom.:
56
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0510
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00590
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00146
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000191
Gnomad OTH
AF:
0.00913
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0148
AC:
2246
AN:
152020
Hom.:
56
Cov.:
31
AF XY:
0.0142
AC XY:
1056
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.0510
Gnomad4 AMR
AF:
0.00590
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00125
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000191
Gnomad4 OTH
AF:
0.00904
Alfa
AF:
0.00904
Hom.:
8
Bravo
AF:
0.0168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
2.8
DANN
Benign
0.46

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1323855; hg19: chr11-35768158; API