chr7-143442717-C-G

Variant names:

• chr7-143442717-C-G
• rs10241042
• ENST00000429289.5:n.206+27518C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429289.5(EPHA1-AS1):​n.206+27518C>G variant causes a intron 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 ENST00000429289.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 2 publications found

Genes affected

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

ENSG00000309456 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
EPHA1-AS1	NR_033897.1	n.206+27518C>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.206+27518C>G		intron_variant	Intron 2 of 4	1
EPHA1-AS1	ENST00000690912.2	n.227+27518C>G		intron_variant	Intron 2 of 2
EPHA1-AS1	ENST00000703017.1	n.205+27518C>G		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.0671 AC: 2785 AN: 41502

American (AMR) AF: 0.287 AC: 4375 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 835 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1526 AN: 5154

South Asian (SAS) AF: 0.298 AC: 1427 AN: 4790

European-Finnish (FIN) AF: 0.253 AC: 2662 AN: 10530

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20977 AN: 67954

Other (OTH) AF: 0.242 AC: 511 AN: 2112

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
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10241042; hg19: chr7-143139810;