6-52580583-T-C

Variant names:

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

Variant summary

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

The ENST00000606558.7(TRAM2-AS1):​n.679+974T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,200 control chromosomes in the GnomAD database, including 51,849 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 0.82 (51849 hom., cov: 32)
• Consequence: TRAM2-AS1 ENST00000606558.7 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606558.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRAM2-AS1	NR_103446.1		n.1427+974T>C		intron	N/A
	TRAM2-AS1	NR_103447.1		n.933+974T>C		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.822 AC: 125044 AN: 152082 Hom.: 51798 Cov.: 32

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.822 AC: 125147 AN: 152200 Hom.: 51849 Cov.: 32 AF XY: 0.819 AC XY: 60963 AN XY: 74410

African (AFR) AF: 0.893 AC: 37088 AN: 41532

American (AMR) AF: 0.673 AC: 10301 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2823 AN: 3470

East Asian (EAS) AF: 0.681 AC: 3520 AN: 5166

South Asian (SAS) AF: 0.849 AC: 4096 AN: 4824

European-Finnish (FIN) AF: 0.835 AC: 8841 AN: 10594

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55756 AN: 68000

Other (OTH) AF: 0.801 AC: 1690 AN: 2110

Alfa AF: 0.797 Hom.: 2530

Bravo AF: 0.806

Asia WGS AF: 0.769 AC: 2677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.57
PhyloP100		-0.71

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6901146;

hg19: chr6-52445381;