Genetic Variant NM_017583.6:c.670-27G>C (chr11-35685232-G-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_017583.6(TRIM44):c.670-27G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,596,814 control chromosomes in the GnomAD database, including 18,953 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.12 ( 1416 hom., cov: 33)

Exomes 𝑓: 0.15 ( 17537 hom. )

Consequence

TRIM44
NM_017583.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.99

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]

TRIM44 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

This position, referring to a specific DNA site, is a probable branch point but is likely benign (scored 3 / 10, using the threshold of <=3). The score ranges from 0 to 10, with values ≤3 considered benign and >5 classified as pathogenic. Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 11-35685232-G-C is Benign according to our data. Variant chr11-35685232-G-C is described in ClinVar as [Benign]. Clinvar id is 1342269.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM44	NM_017583.6 link	c.670-27G>C		intron_variant	Intron 1 of 4	ENST00000299413.7	NP_060053.2
TRIM44	XM_006718254.2 link	c.670-27G>C		intron_variant	Intron 1 of 3		XP_006718317.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM44	ENST00000299413.7 link	c.670-27G>C		intron_variant	Intron 1 of 4	1	NM_017583.6	ENSP00000299413.5		Q96DX7

Frequencies

GnomAD3 genomes

AF:

0.123

AC:

18668

AN:

152174

Hom.:

1413

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0426

Gnomad AMI

AF:

0.0593

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.0650

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.218

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.131

GnomAD3 exomes

AF:

0.137

AC:

34199

AN:

249668

Hom.:

2739

AF XY:

0.140

AC XY:

18863

AN XY:

134880

show subpopulations

Gnomad AFR exome

AF:

0.0387

Gnomad AMR exome

AF:

0.109

Gnomad ASJ exome

AF:

0.117

Gnomad EAS exome

AF:

0.0611

Gnomad SAS exome

AF:

0.0999

Gnomad FIN exome

AF:

0.216

Gnomad NFE exome

AF:

0.168

Gnomad OTH exome

AF:

0.146

GnomAD4 exome

AF:

0.152

AC:

219423

AN:

1444522

Hom.:

17537

Cov.:

AF XY:

0.151

AC XY:

109042

AN XY:

719780

show subpopulations

Gnomad4 AFR exome

AF:

0.0335

Gnomad4 AMR exome

AF:

0.111

Gnomad4 ASJ exome

AF:

0.114

Gnomad4 EAS exome

AF:

0.0753

Gnomad4 SAS exome

AF:

0.105

Gnomad4 FIN exome

AF:

0.221

Gnomad4 NFE exome

AF:

0.162

Gnomad4 OTH exome

AF:

0.141

GnomAD4 genome

AF:

0.123

AC:

18682

AN:

152292

Hom.:

1416

Cov.:

AF XY:

0.124

AC XY:

9230

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.0425

Gnomad4 AMR

AF:

0.106

Gnomad4 ASJ

AF:

0.112

Gnomad4 EAS

AF:

0.0652

Gnomad4 SAS

AF:

0.103

Gnomad4 FIN

AF:

0.218

Gnomad4 NFE

AF:

0.168

Gnomad4 OTH

AF:

0.136

Alfa

AF:

0.0987

Hom.:

211

Bravo

AF:

0.110

Asia WGS

AF:

0.0870

AC:

300

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Aniridia 3

Benign:1

Sep 10, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.44

BranchPoint Hunter

3.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over