7-143410783-C-T

Variant names:

• chr7-143410783-C-T
• rs11762262
• ENST00000429289.5:n.74+2897C>T

Variant summary

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

The ENST00000841079.1(EPHA1-AS1):​n.26C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 151,968 control chromosomes in the GnomAD database, including 3,383 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 0.21 (3383 hom., cov: 30)
• Consequence: EPHA1-AS1 ENST00000841079.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 14 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841079.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPHA1-AS1	NR_033897.1		n.74+2897C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPHA1-AS1	ENST00000429289.5	TSL:1	n.74+2897C>T		intron	N/A
	EPHA1-AS1	ENST00000841079.1		n.26C>T		non_coding_transcript_exon	Exon 1 of 3
	EPHA1-AS1	ENST00000841080.1		n.20C>T		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31207 AN: 151852 Hom.: 3374 Cov.: 30

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.206 AC: 31244 AN: 151968 Hom.: 3383 Cov.: 30 AF XY: 0.202 AC XY: 15024 AN XY: 74274

African (AFR) AF: 0.242 AC: 10011 AN: 41394

American (AMR) AF: 0.195 AC: 2979 AN: 15270

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

East Asian (EAS) AF: 0.147 AC: 761 AN: 5162

South Asian (SAS) AF: 0.261 AC: 1255 AN: 4814

European-Finnish (FIN) AF: 0.148 AC: 1566 AN: 10576

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13658 AN: 67968

Other (OTH) AF: 0.178 AC: 376 AN: 2108

Alfa AF: 0.199 Hom.: 11724

Bravo AF: 0.208

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11762262;

hg19: chr7-143107876;