rs7800937

Variant names:

• chr7-143396214-G-A
• rs7800937
• NM_005232.5:c.1897+171C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005232.5(EPHA1):​c.1897+171C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 152,286 control chromosomes in the GnomAD database, including 65,175 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 0.92 (65175 hom., cov: 33)
• Consequence: EPHA1 NM_005232.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991

Genes affected

EPHA1 (HGNC:3385): (EPH receptor A1) This gene belongs to the ephrin receptor subfamily of the protein-tyrosine kinase family. EPH and EPH-related receptors have been implicated in mediating developmental events, particularly in the nervous system. Receptors in the EPH subfamily typically have a single kinase domain and an extracellular region containing a Cys-rich domain and 2 fibronectin type III repeats. The ephrin receptors are divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. This gene is expressed in some human cancer cell lines and has been implicated in carcinogenesis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPHA1	NM_005232.5	c.1897+171C>T		intron_variant	Intron 11 of 17	ENST00000275815.4	NP_005223.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHA1	ENST00000275815.4	c.1897+171C>T		intron_variant	Intron 11 of 17	1	NM_005232.5	ENSP00000275815.3
EPHA1	ENST00000488068.5	n.2049+171C>T		intron_variant	Intron 10 of 15	1
EPHA1	ENST00000494989.1	n.297+171C>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140650 AN: 152168 Hom.: 65121 Cov.: 33

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.969

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.951

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

GnomAD4 genome AF: 0.924 AC: 140764 AN: 152286 Hom.: 65175 Cov.: 33 AF XY: 0.923 AC XY: 68747 AN XY: 74446

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.969

Gnomad4 ASJ AF: 0.968

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.986

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.922

Gnomad4 OTH AF: 0.951

Alfa AF: 0.914 Hom.: 10434

Bravo AF: 0.933

Asia WGS AF: 0.981 AC: 3409 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.39

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

Other links and lift over

dbSNP: rs7800937; hg19: chr7-143093307;