1-231190340-G-A

Position:

• chr1-231190340-G-A

Variant summary

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

The NM_001004342.5(TRIM67):​c.1045-7031G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,992 control chromosomes in the GnomAD database, including 29,181 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 0.59 (29181 hom., cov: 31)
• Consequence: TRIM67 NM_001004342.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

Genes affected

TRIM67 (HGNC:31859): (tripartite motif containing 67) Predicted to enable zinc ion binding activity. Predicted to be involved in regulation of protein localization. Predicted to act upstream of or within negative regulation of Ras protein signal transduction; positive regulation of neuron projection development; and positive regulation of ubiquitin-dependent protein catabolic process. Predicted to be located in cytoplasm and cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM67	NM_001004342.5	c.1045-7031G>A		intron_variant		ENST00000366653.6
TRIM67	NM_001300889.3	c.859-7031G>A		intron_variant
TRIM67	NM_001410937.1	c.1045-7031G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM67	ENST00000366653.6	c.1045-7031G>A		intron_variant		1	NM_001004342.5	A1
TRIM67	ENST00000449018.7	c.859-7031G>A		intron_variant		1
TRIM67	ENST00000444294.7	c.1045-7031G>A		intron_variant		5		P3

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88858 AN: 151874 Hom.: 29114 Cov.: 31

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.585 AC: 88982 AN: 151992 Hom.: 29181 Cov.: 31 AF XY: 0.588 AC XY: 43704 AN XY: 74280

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.564

Alfa AF: 0.452 Hom.: 33353

Bravo AF: 0.607

Asia WGS AF: 0.654 AC: 2278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.51
DANN	Benign	0.36

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: rs1998027; hg19: chr1-231326086;