rs1771316

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018212.6(ENAH):​c.*4497T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.936 in 152,180 control chromosomes in the GnomAD database, including 66,794 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 0.94 ( 66792 hom., cov: 31)
Exomes 𝑓: 1.0 ( 2 hom. )

Consequence

ENAH
NM_018212.6 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ENAHNM_018212.6 linkuse as main transcriptc.*4497T>G 3_prime_UTR_variant 14/14 ENST00000366843.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENAHENST00000366843.7 linkuse as main transcriptc.*4497T>G 3_prime_UTR_variant 14/141 NM_018212.6 P2Q8N8S7-2
ENAHENST00000366844.7 linkuse as main transcriptc.*4497T>G 3_prime_UTR_variant 15/151 A2Q8N8S7-1
ENAHENST00000696609.1 linkuse as main transcriptc.*4497T>G 3_prime_UTR_variant 12/12

Frequencies

GnomAD3 genomes
AF:
0.936
AC:
142389
AN:
152058
Hom.:
66742
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.886
Gnomad AMI
AF:
0.982
Gnomad AMR
AF:
0.958
Gnomad ASJ
AF:
0.953
Gnomad EAS
AF:
0.910
Gnomad SAS
AF:
0.920
Gnomad FIN
AF:
0.968
Gnomad MID
AF:
0.968
Gnomad NFE
AF:
0.959
Gnomad OTH
AF:
0.944
GnomAD4 exome
AF:
1.00
AC:
4
AN:
4
Hom.:
2
Cov.:
0
AC XY:
0
AN XY:
0
show subpopulations
Gnomad4 FIN exome
AF:
1.00
Gnomad4 NFE exome
AF:
1.00
GnomAD4 genome
AF:
0.936
AC:
142496
AN:
152176
Hom.:
66792
Cov.:
31
AF XY:
0.937
AC XY:
69686
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.886
Gnomad4 AMR
AF:
0.958
Gnomad4 ASJ
AF:
0.953
Gnomad4 EAS
AF:
0.910
Gnomad4 SAS
AF:
0.921
Gnomad4 FIN
AF:
0.968
Gnomad4 NFE
AF:
0.959
Gnomad4 OTH
AF:
0.944
Alfa
AF:
0.954
Hom.:
84496
Bravo
AF:
0.934
Asia WGS
AF:
0.928
AC:
3228
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.82
DANN
Benign
0.49

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1771316; hg19: chr1-225680980; COSMIC: COSV52866205; COSMIC: COSV52866205; API