Variant 6-52600653-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.717

Variant links:

Genes affected

LOC124901330 (HGNC:):

LOC124901330 links:

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

TRAM2-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124901330	XR_007059610.1 link	n.4492G>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	Effect
TRAM2-AS1	ENST00000653743.1 link	n.1399+21044G>T	intron_variant
TRAM2-AS1	ENST00000653877.1 link	n.579+21044G>T	intron_variant
TRAM2-AS1	ENST00000667402.1 link	n.1315+21044G>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.515

AC:

78185

AN:

151782

Hom.:

20540

Cov.:

show subpopulations

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.:

AF XY:

0.510

AC XY:

37884

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.603

Gnomad4 AMR

AF:

0.466

Gnomad4 ASJ

AF:

0.548

Gnomad4 EAS

AF:

0.394

Gnomad4 SAS

AF:

0.539

Gnomad4 FIN

AF:

0.448

Gnomad4 NFE

AF:

0.488

Gnomad4 OTH

AF:

0.519

Alfa

AF:

0.452

Hom.:

3481

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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over