7-143470030-A-G

Variant names:

• chr7-143470030-A-G
• rs2966712
• ENST00000429289.5:n.207-34744A>G

Variant summary

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

The ENST00000429289.5(EPHA1-AS1):​n.207-34744A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 152,194 control chromosomes in the GnomAD database, including 37,200 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 0.70 (37200 hom., cov: 33)
• Consequence: EPHA1-AS1 ENST00000429289.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPHA1-AS1	NR_033897.1	n.207-34744A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHA1-AS1	ENST00000429289.5	n.207-34744A>G		intron_variant	Intron 2 of 4	1
EPHA1-AS1	ENST00000690912.1	n.228-25936A>G		intron_variant	Intron 2 of 2
EPHA1-AS1	ENST00000703017.1	n.206-25936A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105854 AN: 152076 Hom.: 37156 Cov.: 33

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.696 AC: 105956 AN: 152194 Hom.: 37200 Cov.: 33 AF XY: 0.702 AC XY: 52253 AN XY: 74428

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.696

Alfa AF: 0.684 Hom.: 16142

Bravo AF: 0.702

Asia WGS AF: 0.815 AC: 2832 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	0.62
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2966712; hg19: chr7-143167123;