rs7122620

chr11-5662337-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047427783.1(TRIM5):c.794+3319C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 152,064 control chromosomes in the GnomAD database, including 19,593 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 0.50 (19593 hom., cov: 32)
• Consequence: TRIM5 XM_047427783.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

Genes affected

TRIM5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM5	XM_047427783.1	c.794+3319C>T		intron_variant
TRIM5	XM_047427784.1	c.744+15867C>T		intron_variant
TRIM5	XR_001748014.3	n.1163+3319C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000642298.1	n.151+3319C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75717 AN: 151946 Hom.: 19590 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.498 AC: 75747 AN: 152064 Hom.: 19593 Cov.: 32 AF XY: 0.489 AC XY: 36374 AN XY: 74320

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.503

Alfa AF: 0.535 Hom.: 29493

Bravo AF: 0.491

Asia WGS AF: 0.293 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.3
Dann	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7122620; hg19: chr11-5683567;