chr3-97472495-C-T

Variant summary

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

The NM_001080448.3(EPHA6):​c.1895-2857C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 151,646 control chromosomes in the GnomAD database, including 2,182 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 0.15 ( 2182 hom., cov: 32)

Consequence

EPHA6
NM_001080448.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0660
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=-0.96).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EPHA6NM_001080448.3 linkuse as main transcriptc.1895-2857C>T intron_variant ENST00000389672.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EPHA6ENST00000389672.10 linkuse as main transcriptc.1895-2857C>T intron_variant 1 NM_001080448.3 P1

Frequencies

GnomAD3 genomes
AF:
0.147
AC:
22346
AN:
151528
Hom.:
2176
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.241
Gnomad AMI
AF:
0.00548
Gnomad AMR
AF:
0.248
Gnomad ASJ
AF:
0.0386
Gnomad EAS
AF:
0.113
Gnomad SAS
AF:
0.0894
Gnomad FIN
AF:
0.0861
Gnomad MID
AF:
0.0605
Gnomad NFE
AF:
0.0926
Gnomad OTH
AF:
0.128
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.148
AC:
22384
AN:
151646
Hom.:
2182
Cov.:
32
AF XY:
0.148
AC XY:
10939
AN XY:
74132
show subpopulations
Gnomad4 AFR
AF:
0.241
Gnomad4 AMR
AF:
0.248
Gnomad4 ASJ
AF:
0.0386
Gnomad4 EAS
AF:
0.113
Gnomad4 SAS
AF:
0.0879
Gnomad4 FIN
AF:
0.0861
Gnomad4 NFE
AF:
0.0926
Gnomad4 OTH
AF:
0.130
Alfa
AF:
0.105
Hom.:
1203
Bravo
AF:
0.165
Asia WGS
AF:
0.132
AC:
460
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
2.6
DANN
Benign
0.61

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: rs6801975; hg19: chr3-97191339; API