rs12703526

Positions:

• chr7-143410495-G-T

Variant summary

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

The NR_033897.1(EPHA1-AS1):​n.74+2609G>T variant causes a intron, non coding transcript 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 NR_033897.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700

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 (NFE) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPHA1-AS1	NR_033897.1	n.74+2609G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPHA1-AS1	ENST00000429289.5	n.74+2609G>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.464

Alfa AF: 0.492 Hom.: 18233

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12703526; hg19: chr7-143107588;