NM_004428.3:c.*154G>T

Variant names:

• chr1-155134221-G-T
• rs12904
• NM_004428.3:c.*154G>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_004428.3(EFNA1):​c.*154G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: EFNA1 NM_004428.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.11
• Publications: 69 publications found

Genes affected

EFNA1 (HGNC:3221): (ephrin A1) This gene encodes a member of the ephrin (EPH) family. The ephrins and EPH-related receptors comprise the largest subfamily of receptor protein-tyrosine kinases and have been implicated in mediating developmental events, especially in the nervous system and in erythropoiesis. Based on their structures and sequence relationships, ephrins are divided into the ephrin-A (EFNA) class, which are anchored to the membrane by a glycosylphosphatidylinositol linkage, and the ephrin-B (EFNB) class, which are transmembrane proteins. This gene encodes an EFNA class ephrin which binds to the EPHA2, EPHA4, EPHA5, EPHA6, and EPHA7 receptors. Two transcript variants that encode different isoforms were identified through sequence analysis. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004428.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFNA1	NM_004428.3	MANE Select	c.*154G>T		3_prime_UTR	Exon 5 of 5	NP_004419.2
	EFNA1	NM_182685.2		c.*154G>T		3_prime_UTR	Exon 4 of 4	NP_872626.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFNA1	ENST00000368407.8	TSL:1 MANE Select	c.*154G>T		3_prime_UTR	Exon 5 of 5	ENSP00000357392.3
	EFNA1	ENST00000368406.2	TSL:1	c.*154G>T		3_prime_UTR	Exon 4 of 4	ENSP00000357391.2
	EFNA1	ENST00000469878.5	TSL:3	n.1023G>T		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 574992 Hom.: 0 Cov.: 7 AF XY: 0.00 AC XY: 0 AN XY: 301234

African (AFR) AF: 0.00 AC: 0 AN: 15474

American (AMR) AF: 0.00 AC: 0 AN: 25470

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15624

East Asian (EAS) AF: 0.00 AC: 0 AN: 31934

South Asian (SAS) AF: 0.00 AC: 0 AN: 52182

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31998

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2534

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 369388

Other (OTH) AF: 0.00 AC: 0 AN: 30388

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	18
DANN	Benign	0.84
PhyloP100		2.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs12904; hg19: chr1-155106697;