rs12703526

Variant names:

• chr7-143410495-G-T
• rs12703526
• ENST00000429289.5:n.74+2609G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429289.5(EPHA1-AS1):​n.74+2609G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 150,188 control chromosomes in the GnomAD database, including 13,616 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 0.41 (13616 hom., cov: 28)
• Consequence: EPHA1-AS1 ENST00000429289.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700
• Publications: 22 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPHA1-AS1	NR_033897.1	n.74+2609G>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHA1-AS1	ENST00000429289.5	n.74+2609G>T		intron_variant	Intron 1 of 4	1
EPHA1-AS1	ENST00000421648.3	n.329+2605G>T		intron_variant	Intron 1 of 2	2
EPHA1-AS1	ENST00000690912.2	n.95+2605G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.410 AC: 61599 AN: 150068 Hom.: 13605 Cov.: 28

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.410 AC: 61625 AN: 150188 Hom.: 13616 Cov.: 28 AF XY: 0.403 AC XY: 29467 AN XY: 73174

African (AFR) AF: 0.300 AC: 12274 AN: 40892

American (AMR) AF: 0.352 AC: 5308 AN: 15060

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2094 AN: 3468

East Asian (EAS) AF: 0.158 AC: 808 AN: 5118

South Asian (SAS) AF: 0.404 AC: 1925 AN: 4766

European-Finnish (FIN) AF: 0.369 AC: 3653 AN: 9902

Middle Eastern (MID) AF: 0.579 AC: 168 AN: 290

European-Non Finnish (NFE) AF: 0.501 AC: 33949 AN: 67702

Other (OTH) AF: 0.464 AC: 968 AN: 2084

Alfa AF: 0.480 Hom.: 22961

Bravo AF: 0.404

Asia WGS AF: 0.312 AC: 1086 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	5.1
DANN	Benign	0.55
PhyloP100		0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12703526; hg19: chr7-143107588;