Variant rs2239331 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000636266.1(ENSG00000283213):n.548C>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 0.505 in 151,938 control chromosomes in the GnomAD database, including 21,410 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 0.50 ( 21399 hom., cov: 30)

Exomes 𝑓: 0.49 ( 11 hom. )

Consequence

ENSG00000283213
ENST00000636266.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.162

Variant links:

Genes affected

ENSG00000283213 (HGNC:):

ENSG00000283213 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
LOC107984851	XR_001752349.2 linkuse as main transcript	n.285C>T	non_coding_transcript_exon_variant	2/4
LOC107984851	XR_005647011.2 linkuse as main transcript	n.1295C>T	non_coding_transcript_exon_variant	2/4
LOC107984851	XR_007065029.1 linkuse as main transcript	n.208C>T	non_coding_transcript_exon_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000283213	ENST00000636266.1 linkuse as main transcript	n.548C>T		non_coding_transcript_exon_variant	1/2	5
ENSG00000283213	ENST00000636354.1 linkuse as main transcript	n.69C>T		non_coding_transcript_exon_variant	1/3	5

Frequencies

GnomAD3 genomes

AF:

0.505

AC:

76593

AN:

151746

Hom.:

21369

Cov.:

show subpopulations

Gnomad AFR

AF:

0.763

Gnomad AMI

AF:

0.381

Gnomad AMR

AF:

0.438

Gnomad ASJ

AF:

0.333

Gnomad EAS

AF:

0.416

Gnomad SAS

AF:

0.471

Gnomad FIN

AF:

0.380

Gnomad MID

AF:

0.538

Gnomad NFE

AF:

0.402

Gnomad OTH

AF:

0.490

GnomAD4 exome

AF:

0.486

AC:

AN:

Hom.:

Cov.:

AF XY:

0.457

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.400

Gnomad4 NFE exome

AF:

0.543

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.505

AC:

76674

AN:

151864

Hom.:

21399

Cov.:

AF XY:

0.502

AC XY:

37270

AN XY:

74214

show subpopulations

Gnomad4 AFR

AF:

0.763

Gnomad4 AMR

AF:

0.438

Gnomad4 ASJ

AF:

0.333

Gnomad4 EAS

AF:

0.415

Gnomad4 SAS

AF:

0.471

Gnomad4 FIN

AF:

0.380

Gnomad4 NFE

AF:

0.402

Gnomad4 OTH

AF:

0.490

Alfa

AF:

0.426

Hom.:

19032

Bravo

AF:

0.522

Asia WGS

AF:

0.497

AC:

1731

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.2

DANN

Benign

0.75

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