Variant 7-143442717-C-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_033897.1(EPHA1-AS1):n.206+27518C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,984 control chromosomes in the GnomAD database, including 4,985 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 0.23 ( 4985 hom., cov: 31)

Consequence

EPHA1-AS1
NR_033897.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.243

Variant links:

Genes affected

EPHA1-AS1 (HGNC:27799): (EPHA1 antisense RNA 1)

EPHA1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPHA1-AS1	NR_033897.1 linkuse as main transcript	n.206+27518C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
EPHA1-AS1	ENST00000429289.5 linkuse as main transcript	n.206+27518C>G	intron_variant, non_coding_transcript_variant	1
EPHA1-AS1	ENST00000690912.1 linkuse as main transcript	n.227+27518C>G	intron_variant, non_coding_transcript_variant
EPHA1-AS1	ENST00000703017.1 linkuse as main transcript	n.205+27518C>G	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35323

AN:

151866

Hom.:

4979

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0672

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.297

Gnomad SAS

AF:

0.296

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.309

Gnomad OTH

AF:

0.242

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

GnomAD4 genome

AF:

0.233

AC:

35340

AN:

151984

Hom.:

4985

Cov.:

AF XY:

0.232

AC XY:

17214

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.0671

Gnomad4 AMR

AF:

0.287

Gnomad4 ASJ

AF:

0.241

Gnomad4 EAS

AF:

0.296

Gnomad4 SAS

AF:

0.298

Gnomad4 FIN

AF:

0.253

Gnomad4 NFE

AF:

0.309

Gnomad4 OTH

AF:

0.242

Alfa

AF:

0.258

Hom.:

748

Bravo

AF:

0.224

Asia WGS

AF:

0.268

AC:

935

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.4

DANN

Benign

0.74

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