9-98088685-A-G

Position:

• chr9-98088685-A-G

Variant summary

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

The NM_014788.4(TRIM14):​c.794-680T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,254 control chromosomes in the GnomAD database, including 4,060 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 0.22 (4060 hom., cov: 33)
• Consequence: TRIM14 NM_014788.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96

Genes affected

TRIM14 (HGNC:16283): (tripartite motif containing 14) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein localizes to cytoplasmic bodies and its function has not been determined. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM14	NM_014788.4	c.794-680T>C		intron_variant		ENST00000341469.7	NP_055603.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM14	ENST00000341469.7	c.794-680T>C		intron_variant		1	NM_014788.4	ENSP00000344208	P1
TRIM14	ENST00000342043.3	c.794-680T>C		intron_variant		1		ENSP00000343990	P1
TRIM14	ENST00000375098.7	c.794-680T>C		intron_variant		2		ENSP00000364239	P1
TRIM14	ENST00000475147.1	c.*177-680T>C		intron_variant, NMD_transcript_variant		2		ENSP00000428805

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33949 AN: 152136 Hom.: 4056 Cov.: 33

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0864

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.223 AC: 33978 AN: 152254 Hom.: 4060 Cov.: 33 AF XY: 0.218 AC XY: 16206 AN XY: 74442

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.0880

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.237

Alfa AF: 0.232 Hom.: 887

Bravo AF: 0.234

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.55

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: rs10818472; hg19: chr9-100850967;