rs3733418

Variant names:

• chr4-164957183-A-C
• NM_001012414.3:c.526-2087T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-164957183-A-C
• chr4-164957183-A-G
• chr4-164957183-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001012414.3(TRIM61):​c.526-2087T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TRIM61 NM_001012414.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

TRIM61 (HGNC:24339): (tripartite motif containing 61) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in innate immune response; protein ubiquitination; and regulation of gene expression. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

FAM218A (HGNC:26466): (family with sequence similarity 218 member A)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.04165563).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM61	NM_001012414.3	c.526-2087T>G		intron_variant	Intron 3 of 4	ENST00000329314.6	NP_001012414.1
FAM218A	NR_160935.1	n.236A>C		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM61	ENST00000329314.6	c.526-2087T>G		intron_variant	Intron 3 of 4	1	NM_001012414.3	ENSP00000332288.5
FAM218A	ENST00000648094.1	n.236A>C		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.080
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	5.0
DANN	Benign	0.26
DEOGEN2	Benign	0.054	T
Eigen	Benign	-1.7
Eigen_PC	Benign	-1.8
FATHMM_MKL	Benign	0.0016	N
LIST_S2	Benign	0.16	T
M_CAP	Benign	0.0020	T
MetaRNN	Benign	0.042	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N
PROVEAN	Uncertain	-4.0	D
REVEL	Benign	0.063
Polyphen		0.0	B
Vest4		0.093
MutPred		0.20		Loss of sheet (P = 0.0228);
MVP		0.014
MPC		1.1
ClinPred		0.056	T
GERP RS		-1.1
Varity_R		0.34
gMVP		0.024

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr4-165878335;