3-32845663-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TRIM71	NM_001039111.3	c.852+26731A>G		intron_variant		ENST00000383763.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM71	ENST00000383763.6	c.852+26731A>G		intron_variant		1	NM_001039111.3	P1

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

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0221

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.204

Alfa AF: 0.166 Hom.: 602

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

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

Other links and lift over

dbSNP: rs1878887; hg19: chr3-32887155;