rs11771145

chr7-143413669-G-Achr7-143413669-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.75-1399G>A 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 0.414 in 151,954 control chromosomes in the GnomAD database, including 13,661 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 (13661 hom., cov: 32)
• Consequence: EPHA1-AS1 NR_033897.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPHA1-AS1	NR_033897.1	n.75-1399G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPHA1-AS1	ENST00000429289.5	n.75-1399G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62877 AN: 151836 Hom.: 13638 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.414 AC: 62936 AN: 151954 Hom.: 13661 Cov.: 32 AF XY: 0.415 AC XY: 30795 AN XY: 74294

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.375

Alfa AF: 0.352 Hom.: 21433

Bravo AF: 0.422

Asia WGS AF: 0.418 AC: 1454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.2
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11771145; hg19: chr7-143110762;