1-225488869-G-A

Position:

• chr1-225488869-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000366843.7(ENAH):​c.*8906C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,204 control chromosomes in the GnomAD database, including 1,853 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 0.13 (1853 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: ENAH ENST00000366843.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

Genes affected

ENAH (HGNC:18271): (ENAH actin regulator) This gene encodes a member of the enabled/ vasodilator-stimulated phosphoprotein. Members of this gene family are involved in actin-based motility. This protein is involved in regulating the assembly of actin filaments and modulates cell adhesion and motility. Alternate splice variants of this gene have been correlated with tumor invasiveness in certain tissues and these variants may serve as prognostic markers. A pseudogene of this gene is found on chromosome 3. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENAH	NM_018212.6	c.*8906C>T		3_prime_UTR_variant	14/14	ENST00000366843.7	NP_060682.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENAH	ENST00000366843.7	c.*8906C>T		3_prime_UTR_variant	14/14	1	NM_018212.6	ENSP00000355808	P2
ENAH	ENST00000366844.7	c.*8906C>T		3_prime_UTR_variant	15/15	1		ENSP00000355809	A2
ENAH	ENST00000696609.1	c.*8906C>T		3_prime_UTR_variant	12/12			ENSP00000512753

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20140 AN: 152080 Hom.: 1856 Cov.: 32

Gnomad AFR AF: 0.0315

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.134

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

Gnomad4 NFE exome AF: 0.167

GnomAD4 genome AF: 0.132 AC: 20129 AN: 152198 Hom.: 1853 Cov.: 32 AF XY: 0.136 AC XY: 10144 AN XY: 74404

Gnomad4 AFR AF: 0.0314

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0651

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.131

Alfa AF: 0.140 Hom.: 726

Bravo AF: 0.126

Asia WGS AF: 0.222 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.62
DANN	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12043633; hg19: chr1-225676571;