chr1-16162611-C-T

Variant names:

• chr1-16162611-C-T
• rs729402
• NR_187272.1:n.1861C>T

Variant summary

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

The NR_187272.1(EPHA2-AS1):​n.1861C>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 0.462 in 152,122 control chromosomes in the GnomAD database, including 17,643 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 0.46 (17643 hom., cov: 34)
• Consequence: EPHA2-AS1 NR_187272.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 3 publications found

Genes affected

EPHA2-AS1 (HGNC:40216): (EPHA2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPHA2-AS1	NR_187272.1	n.1861C>T		non_coding_transcript_exon_variant	Exon 3 of 3
EPHA2-AS1	NR_187273.1	n.751-1860C>T		intron_variant	Intron 2 of 2
EPHA2-AS1	NR_187275.1	n.751-2145C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHA2-AS1	ENST00000793379.1	n.527-5565C>T		intron_variant	Intron 1 of 2
EPHA2-AS1	ENST00000793381.1	n.274+3185C>T		intron_variant	Intron 2 of 3
EPHA2-AS1	ENST00000793382.1	n.287-1860C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70122 AN: 152004 Hom.: 17592 Cov.: 34

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.462 AC: 70232 AN: 152122 Hom.: 17643 Cov.: 34 AF XY: 0.458 AC XY: 34066 AN XY: 74368

African (AFR) AF: 0.660 AC: 27383 AN: 41508

American (AMR) AF: 0.464 AC: 7101 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1669 AN: 3472

East Asian (EAS) AF: 0.142 AC: 729 AN: 5148

South Asian (SAS) AF: 0.426 AC: 2055 AN: 4824

European-Finnish (FIN) AF: 0.308 AC: 3266 AN: 10602

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26568 AN: 67954

Other (OTH) AF: 0.463 AC: 980 AN: 2116

Alfa AF: 0.241 Hom.: 486

Bravo AF: 0.477

Asia WGS AF: 0.335 AC: 1164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0060
DANN	Benign	0.71
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs729402; hg19: chr1-16489106; COSMIC: COSV70280909;