rs6925912

Variant names:

• chr6-25976699-G-A
• rs6925912
• NM_006355.5:c.874+3414G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRIM38	NM_006355.5	c.874+3414G>A		intron_variant	Intron 7 of 7	ENST00000357085.5	NP_006346.1
TRIM38	XM_047418080.1	c.*1224G>A		3_prime_UTR_variant	Exon 9 of 9		XP_047274036.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM38	ENST00000357085.5	c.874+3414G>A		intron_variant	Intron 7 of 7	1	NM_006355.5	ENSP00000349596.2

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

African (AFR) AF: 0.299 AC: 12390 AN: 41444

American (AMR) AF: 0.162 AC: 2476 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 942 AN: 3468

East Asian (EAS) AF: 0.0810 AC: 419 AN: 5176

South Asian (SAS) AF: 0.212 AC: 1022 AN: 4812

European-Finnish (FIN) AF: 0.0850 AC: 899 AN: 10580

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10046 AN: 68014

Other (OTH) AF: 0.206 AC: 436 AN: 2112

Alfa AF: 0.169 Hom.: 8247

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
PhyloP100		-0.010
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6925912; hg19: chr6-25976927;