6-25976699-G-A

Position:

• chr6-25976699-G-A

Variant summary

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

The NM_006355.5(TRIM38):​c.874+3414G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,084 control chromosomes in the GnomAD database, including 3,236 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 0.19 (3236 hom., cov: 32)
• Consequence: TRIM38 NM_006355.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

Genes affected

TRIM38 (HGNC:10059): (tripartite motif containing 38) This gene encodes a member of the tripartite motif (TRIM) family. The encoded protein contains a RING-type zinc finger, B box-type zinc finger and SPRY domain. The function of this protein has not been identified. A pseudogene of this gene is located on the long arm of chromosome 4. [provided by RefSeq, Jul 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM38	NM_006355.5	c.874+3414G>A		intron_variant		ENST00000357085.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM38	ENST00000357085.5	c.874+3414G>A		intron_variant		1	NM_006355.5	P1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28799 AN: 151966 Hom.: 3227 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.0850

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.190 AC: 28830 AN: 152084 Hom.: 3236 Cov.: 32 AF XY: 0.186 AC XY: 13801 AN XY: 74350

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0810

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.0850

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.206

Alfa AF: 0.170 Hom.: 3334

Bravo AF: 0.199

Asia WGS AF: 0.140 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.50

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: rs6925912; hg19: chr6-25976927;