rs9310995

Variant names:

• chr3-32887623-T-C
• rs9310995
• NM_001039111.3:c.1155+1555T>C

Variant summary

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

The NM_001039111.3(TRIM71):​c.1155+1555T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,602 control chromosomes in the GnomAD database, including 14,508 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 0.43 (14508 hom., cov: 29)
• Consequence: TRIM71 NM_001039111.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 10 publications found

Genes affected

TRIM71 (HGNC:32669): (tripartite motif containing 71) The protein encoded by this gene is an E3 ubiquitin-protein ligase that binds with miRNAs and maintains the growth and upkeep of embryonic stem cells. This gene also is involved in the G1-S phase transition of the cell cycle. [provided by RefSeq, Dec 2015]

TRIM71 Gene-Disease associations (from GenCC):

• hydrocephalus, congenital communicating, 1

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM71	NM_001039111.3	c.1155+1555T>C		intron_variant	Intron 3 of 3	ENST00000383763.6	NP_001034200.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM71	ENST00000383763.6	c.1155+1555T>C		intron_variant	Intron 3 of 3	1	NM_001039111.3	ENSP00000373272.3

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65694 AN: 151482 Hom.: 14483 Cov.: 29

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.434 AC: 65763 AN: 151602 Hom.: 14508 Cov.: 29 AF XY: 0.431 AC XY: 31893 AN XY: 74054

African (AFR) AF: 0.489 AC: 20175 AN: 41246

American (AMR) AF: 0.372 AC: 5671 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1342 AN: 3470

East Asian (EAS) AF: 0.241 AC: 1239 AN: 5150

South Asian (SAS) AF: 0.332 AC: 1594 AN: 4802

European-Finnish (FIN) AF: 0.448 AC: 4696 AN: 10482

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.434 AC: 29464 AN: 67906

Other (OTH) AF: 0.419 AC: 884 AN: 2112

Alfa AF: 0.434 Hom.: 11450

Bravo AF: 0.429

Asia WGS AF: 0.281 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.64
DANN	Benign	0.57
PhyloP100		-0.49
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: rs9310995; hg19: chr3-32929115;