6-52600653-G-T

Variant names:

• chr6-52600653-G-T
• rs6936059
• XR_007059610.1:n.4492G>T

Variant summary

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

The XR_007059610.1(LOC124901330):​n.4492G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,900 control chromosomes in the GnomAD database, including 20,566 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 0.52 (20566 hom., cov: 32)
• Consequence: LOC124901330 XR_007059610.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.717
• Publications: 4 publications found

Genes affected

LOC124901330 (HGNC:):

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901330	XR_007059610.1	n.4492G>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAM2-AS1	ENST00000653743.1	n.1399+21044G>T		intron_variant	Intron 2 of 2
TRAM2-AS1	ENST00000653877.1	n.579+21044G>T		intron_variant	Intron 3 of 4
TRAM2-AS1	ENST00000667402.1	n.1315+21044G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78185 AN: 151782 Hom.: 20540 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.515 AC: 78256 AN: 151900 Hom.: 20566 Cov.: 32 AF XY: 0.510 AC XY: 37884 AN XY: 74238

African (AFR) AF: 0.603 AC: 24991 AN: 41428

American (AMR) AF: 0.466 AC: 7110 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1899 AN: 3464

East Asian (EAS) AF: 0.394 AC: 2036 AN: 5172

South Asian (SAS) AF: 0.539 AC: 2598 AN: 4816

European-Finnish (FIN) AF: 0.448 AC: 4706 AN: 10496

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33152 AN: 67952

Other (OTH) AF: 0.519 AC: 1096 AN: 2110

Alfa AF: 0.456 Hom.: 4127

Bravo AF: 0.516

Asia WGS AF: 0.521 AC: 1814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.53
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs6936059; hg19: chr6-52465451;