7-143412046-T-C

Variant names:

• chr7-143412046-T-C
• rs11767557
• ENST00000429289.5:n.75-3022T>C

Variant summary

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

The ENST00000429289.5(EPHA1-AS1):​n.75-3022T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,142 control chromosomes in the GnomAD database, including 2,766 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 0.18 (2766 hom., cov: 32)
• Consequence: EPHA1-AS1 ENST00000429289.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 106 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPHA1-AS1	NR_033897.1	n.75-3022T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHA1-AS1	ENST00000429289.5	n.75-3022T>C		intron_variant	Intron 1 of 4	1
EPHA1-AS1	ENST00000421648.3	n.330-3022T>C		intron_variant	Intron 1 of 2	2
EPHA1-AS1	ENST00000690912.2	n.96-3022T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28081 AN: 152024 Hom.: 2761 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.185 AC: 28105 AN: 152142 Hom.: 2766 Cov.: 32 AF XY: 0.183 AC XY: 13578 AN XY: 74396

African (AFR) AF: 0.167 AC: 6939 AN: 41492

American (AMR) AF: 0.189 AC: 2895 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3472

East Asian (EAS) AF: 0.148 AC: 765 AN: 5174

South Asian (SAS) AF: 0.261 AC: 1258 AN: 4824

European-Finnish (FIN) AF: 0.148 AC: 1571 AN: 10606

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13695 AN: 67978

Other (OTH) AF: 0.164 AC: 345 AN: 2102

Alfa AF: 0.195 Hom.: 12498

Bravo AF: 0.184

Asia WGS AF: 0.188 AC: 654 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	1.3
DANN	Benign	0.45
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs11767557; hg19: chr7-143109139;