rs12666496

Positions:

• chr7-143471353-A-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.207-33421A>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 0.282 in 152,112 control chromosomes in the GnomAD database, including 6,440 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 0.28 (6440 hom., cov: 32)
• Consequence: EPHA1-AS1 NR_033897.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EPHA1-AS1	NR_033897.1	n.207-33421A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EPHA1-AS1	ENST00000429289.5	n.207-33421A>T		intron_variant, non_coding_transcript_variant		1
EPHA1-AS1	ENST00000690912.1	n.228-24613A>T		intron_variant, non_coding_transcript_variant
EPHA1-AS1	ENST00000703017.1	n.206-24613A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42823 AN: 151996 Hom.: 6425 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.282 AC: 42869 AN: 152112 Hom.: 6440 Cov.: 32 AF XY: 0.276 AC XY: 20553 AN XY: 74352

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.295

Alfa AF: 0.281 Hom.: 774

Bravo AF: 0.283

Asia WGS AF: 0.202 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
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: rs12666496; hg19: chr7-143168446;