rs7129170

Variant names:

• chr11-35732916-A-G
• rs7129170
• NM_017583.6:c.988-2510A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017583.6(TRIM44):​c.988-2510A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,216 control chromosomes in the GnomAD database, including 1,490 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 0.12 (1490 hom., cov: 32)
• Consequence: TRIM44 NM_017583.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• Publications: 8 publications found

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 Gene-Disease associations (from GenCC):

• isolated aniridia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• aniridia 3

  Inheritance: AD Classification: LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Ambry Genetics

ENSG00000254919 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM44	NM_017583.6	c.988-2510A>G		intron_variant	Intron 3 of 4	ENST00000299413.7	NP_060053.2
TRIM44	XM_006718254.2	c.748-2510A>G		intron_variant	Intron 2 of 3		XP_006718317.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM44	ENST00000299413.7	c.988-2510A>G		intron_variant	Intron 3 of 4	1	NM_017583.6	ENSP00000299413.5
TRIM44	ENST00000532066.1	n.354-2510A>G		intron_variant	Intron 2 of 3	4
ENSG00000254919	ENST00000730429.1	n.419-8522T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18755 AN: 152100 Hom.: 1485 Cov.: 32

Gnomad AFR AF: 0.0288

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0865

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.123 AC: 18773 AN: 152216 Hom.: 1490 Cov.: 32 AF XY: 0.125 AC XY: 9263 AN XY: 74396

African (AFR) AF: 0.0287 AC: 1194 AN: 41570

American (AMR) AF: 0.107 AC: 1639 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 484 AN: 3468

East Asian (EAS) AF: 0.0867 AC: 450 AN: 5188

South Asian (SAS) AF: 0.118 AC: 571 AN: 4820

European-Finnish (FIN) AF: 0.217 AC: 2299 AN: 10572

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11746 AN: 67996

Other (OTH) AF: 0.136 AC: 286 AN: 2110

Alfa AF: 0.151 Hom.: 5340

Bravo AF: 0.110

Asia WGS AF: 0.103 AC: 355 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7129170; hg19: chr11-35754464;