rs2318155

Variant summary

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

The ENST00000389672.10(EPHA6):​c.385+25417T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0316 in 152,236 control chromosomes in the GnomAD database, including 111 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 0.032 ( 111 hom., cov: 32)

Consequence

EPHA6
ENST00000389672.10 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0750
Variant links:
Genes affected
EPHA6 (HGNC:19296): (EPH receptor A6) Predicted to enable transmembrane-ephrin receptor activity. Predicted to be involved in axon guidance; positive regulation of kinase activity; and transmembrane receptor protein tyrosine kinase signaling pathway. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0637 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EPHA6NM_001080448.3 linkuse as main transcriptc.385+25417T>G intron_variant ENST00000389672.10 NP_001073917.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EPHA6ENST00000389672.10 linkuse as main transcriptc.385+25417T>G intron_variant 1 NM_001080448.3 ENSP00000374323 P1
EPHA6ENST00000506569.1 linkuse as main transcriptc.218+25417T>G intron_variant 1 ENSP00000425132
EPHA6ENST00000470610.6 linkuse as main transcriptc.385+25417T>G intron_variant 2 ENSP00000420598

Frequencies

GnomAD3 genomes
AF:
0.0317
AC:
4815
AN:
152118
Hom.:
112
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0194
Gnomad AMI
AF:
0.00658
Gnomad AMR
AF:
0.0297
Gnomad ASJ
AF:
0.0386
Gnomad EAS
AF:
0.0695
Gnomad SAS
AF:
0.0633
Gnomad FIN
AF:
0.00866
Gnomad MID
AF:
0.0633
Gnomad NFE
AF:
0.0377
Gnomad OTH
AF:
0.0378
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0316
AC:
4814
AN:
152236
Hom.:
111
Cov.:
32
AF XY:
0.0304
AC XY:
2259
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.0193
Gnomad4 AMR
AF:
0.0297
Gnomad4 ASJ
AF:
0.0386
Gnomad4 EAS
AF:
0.0696
Gnomad4 SAS
AF:
0.0633
Gnomad4 FIN
AF:
0.00866
Gnomad4 NFE
AF:
0.0377
Gnomad4 OTH
AF:
0.0374
Alfa
AF:
0.0326
Hom.:
11
Bravo
AF:
0.0318
Asia WGS
AF:
0.0870
AC:
303
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.1
DANN
Benign
0.62

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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.

Other links and lift over

dbSNP: rs2318155; hg19: chr3-96559269; API