rs3847124

Variant names:

• chr7-138506779-A-G
• rs3847124
• NM_015905.3:c.483+2371A>G

Variant summary

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

The NM_015905.3(TRIM24):​c.483+2371A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0213 in 152,236 control chromosomes in the GnomAD database, including 94 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 0.021 (94 hom., cov: 32)
• Consequence: TRIM24 NM_015905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

Genes affected

TRIM24 (HGNC:11812): (tripartite motif containing 24) The protein encoded by this gene mediates transcriptional control by interaction with the activation function 2 (AF2) region of several nuclear receptors, including the estrogen, retinoic acid, and vitamin D3 receptors. The protein localizes to nuclear bodies and is thought to associate with chromatin and heterochromatin-associated factors. The protein 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. Two alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

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 = 0.069 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM24	NM_015905.3	c.483+2371A>G		intron_variant	Intron 2 of 18	ENST00000343526.9	NP_056989.2
TRIM24	NM_003852.4	c.483+2371A>G		intron_variant	Intron 2 of 18		NP_003843.3
TRIM24	XM_024446981.2	c.426+2371A>G		intron_variant	Intron 2 of 18		XP_024302749.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM24	ENST00000343526.9	c.483+2371A>G		intron_variant	Intron 2 of 18	1	NM_015905.3	ENSP00000340507.4
TRIM24	ENST00000415680.6	c.483+2371A>G		intron_variant	Intron 2 of 18	1		ENSP00000390829.2
TRIM24	ENST00000497516.5	n.357+2371A>G		intron_variant	Intron 2 of 10	5

Frequencies

GnomAD3 genomes AF: 0.0213 AC: 3237 AN: 152120 Hom.: 94 Cov.: 32

Gnomad AFR AF: 0.0713

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00956

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000867

Gnomad OTH AF: 0.0182

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

GnomAD4 genome AF: 0.0213 AC: 3240 AN: 152236 Hom.: 94 Cov.: 32 AF XY: 0.0204 AC XY: 1522 AN XY: 74428

Gnomad4 AFR AF: 0.0712

Gnomad4 AMR AF: 0.00955

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000867

Gnomad4 OTH AF: 0.0180

Alfa AF: 0.00470 Hom.: 22

Bravo AF: 0.0250

Asia WGS AF: 0.00549 AC: 19 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	0.73
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: rs3847124; hg19: chr7-138191524;