rs6901146

Variant names:

• chr6-52580583-T-A
• rs6901146
• ENST00000453216.2:n.1242+974T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-52580583-T-A
• chr6-52580583-T-C
• chr6-52580583-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000453216.2(TRAM2-AS1):​n.1242+974T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TRAM2-AS1 ENST00000453216.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 1 publications found

Genes affected

TRAM2-AS1 (HGNC:48663): (TRAM2 antisense RNA 1 (head to head))

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453216.2. 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
	TRAM2-AS1	NR_103446.1		n.1427+974T>A		intron	N/A
	TRAM2-AS1	NR_103447.1		n.933+974T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRAM2-AS1	ENST00000453216.2	TSL:3	n.1242+974T>A		intron	N/A
	TRAM2-AS1	ENST00000605910.2	TSL:3	n.803+974T>A		intron	N/A
	TRAM2-AS1	ENST00000606558.7	TSL:2	n.679+974T>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.56
PhyloP100		-0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6901146; hg19: chr6-52445381;