chr3-32845663-A-G

Variant names:

• chr3-32845663-A-G
• rs1878887
• NM_001039111.3:c.852+26731A>G

Variant summary

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

The NM_001039111.3(TRIM71):​c.852+26731A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,860 control chromosomes in the GnomAD database, including 4,638 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 0.24 (4638 hom., cov: 32)
• Consequence: TRIM71 NM_001039111.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM71	NM_001039111.3	c.852+26731A>G		intron_variant	Intron 1 of 3	ENST00000383763.6	NP_001034200.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM71	ENST00000383763.6	c.852+26731A>G		intron_variant	Intron 1 of 3	1	NM_001039111.3	ENSP00000373272.3

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35710 AN: 151752 Hom.: 4638 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.0562

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0220

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.126

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.235 AC: 35741 AN: 151860 Hom.: 4638 Cov.: 32 AF XY: 0.236 AC XY: 17517 AN XY: 74212

African (AFR) AF: 0.344 AC: 14216 AN: 41362

American (AMR) AF: 0.205 AC: 3129 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3470

East Asian (EAS) AF: 0.0221 AC: 114 AN: 5168

South Asian (SAS) AF: 0.228 AC: 1100 AN: 4824

European-Finnish (FIN) AF: 0.232 AC: 2445 AN: 10526

Middle Eastern (MID) AF: 0.129 AC: 37 AN: 286

European-Non Finnish (NFE) AF: 0.200 AC: 13619 AN: 67942

Other (OTH) AF: 0.204 AC: 431 AN: 2108

Alfa AF: 0.180 Hom.: 1135

Bravo AF: 0.232

Asia WGS AF: 0.131 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.6
DANN	Benign	0.79
PhyloP100		-1.1
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: rs1878887; hg19: chr3-32887155;