rs10241042

Positions:

• chr7-143442717-C-G

Variant summary

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

The NR_033897.1(EPHA1-AS1):​n.206+27518C>G 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 0.233 in 151,984 control chromosomes in the GnomAD database, including 4,985 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 0.23 (4985 hom., cov: 31)
• Consequence: EPHA1-AS1 NR_033897.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EPHA1-AS1	NR_033897.1	n.206+27518C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EPHA1-AS1	ENST00000429289.5	n.206+27518C>G		intron_variant, non_coding_transcript_variant		1
EPHA1-AS1	ENST00000690912.1	n.227+27518C>G		intron_variant, non_coding_transcript_variant
EPHA1-AS1	ENST00000703017.1	n.205+27518C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35323 AN: 151866 Hom.: 4979 Cov.: 31

Gnomad AFR AF: 0.0672

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.233 AC: 35340 AN: 151984 Hom.: 4985 Cov.: 31 AF XY: 0.232 AC XY: 17214 AN XY: 74254

Gnomad4 AFR AF: 0.0671

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.242

Alfa AF: 0.258 Hom.: 748

Bravo AF: 0.224

Asia WGS AF: 0.268 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.4
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: rs10241042; hg19: chr7-143139810;