rs2249099

Variant names:

• chr6-30111530-C-A
• rs2249099
• NM_007028.5:c.513+118G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-30111530-C-A
• chr6-30111530-C-G
• chr6-30111530-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007028.5(TRIM31):​c.513+118G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,025,500 control chromosomes in the GnomAD database, including 12,704 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 0.13 (1481 hom., cov: 32)
  • Exomes 𝑓: 0.15 (11223 hom.)
• Consequence: TRIM31 NM_007028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 24 publications found

Genes affected

TRIM31 (HGNC:16289): (tripartite motif containing 31) This gene encodes a protein that functions as an E3 ubiquitin-protein ligase. This gene shows altered expression in certain tumors and may be a negative regulator of cell growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

TRIM31-AS1 (HGNC:39761): (TRIM31 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007028.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM31	NM_007028.5	MANE Select	c.513+118G>T		intron	N/A	NP_008959.3
	TRIM31-AS1	NR_126470.1		n.274-188C>A		intron	N/A
	TRIM31	NR_134870.2		n.623+118G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM31	ENST00000376734.4	TSL:5 MANE Select	c.513+118G>T		intron	N/A	ENSP00000365924.3
	TRIM31	ENST00000493404.1	TSL:2	n.301G>T		non_coding_transcript_exon	Exon 2 of 2
	TRIM31-AS1	ENST00000440874.1	TSL:3	n.274-188C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20070 AN: 152036 Hom.: 1471 Cov.: 32

Gnomad AFR AF: 0.0992

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0951

Gnomad EAS AF: 0.0713

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.153 AC: 133811 AN: 873346 Hom.: 11223 Cov.: 12 AF XY: 0.154 AC XY: 68803 AN XY: 446834

African (AFR) AF: 0.0953 AC: 2008 AN: 21078

American (AMR) AF: 0.172 AC: 5235 AN: 30400

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 1787 AN: 17648

East Asian (EAS) AF: 0.0883 AC: 3207 AN: 36306

South Asian (SAS) AF: 0.184 AC: 11291 AN: 61498

European-Finnish (FIN) AF: 0.148 AC: 6575 AN: 44530

Middle Eastern (MID) AF: 0.0848 AC: 328 AN: 3870

European-Non Finnish (NFE) AF: 0.158 AC: 97356 AN: 617912

Other (OTH) AF: 0.150 AC: 6024 AN: 40104

GnomAD4 genome AF: 0.132 AC: 20094 AN: 152154 Hom.: 1481 Cov.: 32 AF XY: 0.131 AC XY: 9747 AN XY: 74366

African (AFR) AF: 0.0991 AC: 4113 AN: 41510

American (AMR) AF: 0.139 AC: 2129 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0951 AC: 330 AN: 3470

East Asian (EAS) AF: 0.0705 AC: 365 AN: 5174

South Asian (SAS) AF: 0.183 AC: 882 AN: 4828

European-Finnish (FIN) AF: 0.150 AC: 1590 AN: 10576

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10251 AN: 67992

Other (OTH) AF: 0.118 AC: 249 AN: 2110

Alfa AF: 0.155 Hom.: 2287

Bravo AF: 0.127

Asia WGS AF: 0.192 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.0
DANN	Benign	0.73
PhyloP100		-0.037
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs2249099; hg19: chr6-30079307; COSMIC: COSV65059400; COSMIC: COSV65059400;