dbSNP rs6751: ENAH:c.*2917C>T (chr1-225494858-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018212.6(ENAH):c.*2917C>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 0.659 in 152,504 control chromosomes in the GnomAD database, including 33,461 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 0.66 ( 33367 hom., cov: 32)

Exomes 𝑓: 0.67 ( 94 hom. )

Consequence

ENAH
NM_018212.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.903

Publications

7 publications found

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]

ENAH links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018212.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ENAH	NM_018212.6	MANE Select	c.*2917C>T	3_prime_UTR	Exon 14 of 14	NP_060682.2
ENAH	NM_001420159.1		c.*2917C>T	3_prime_UTR	Exon 16 of 16	NP_001407088.1
ENAH	NM_001420160.1		c.*2917C>T	3_prime_UTR	Exon 15 of 15	NP_001407089.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ENAH	ENST00000366843.7	TSL:1 MANE Select	c.*2917C>T	3_prime_UTR	Exon 14 of 14	ENSP00000355808.2
ENAH	ENST00000366844.7	TSL:1	c.*2917C>T	3_prime_UTR	Exon 15 of 15	ENSP00000355809.2
ENAH	ENST00000696609.1		c.*2917C>T	3_prime_UTR	Exon 12 of 12	ENSP00000512753.1

Frequencies

GnomAD3 genomes

AF:

0.659

AC:

100185

AN:

151958

Hom.:

33375

Cov.:

show subpopulations

Gnomad AFR

AF:

0.582

Gnomad AMI

AF:

0.773

Gnomad AMR

AF:

0.664

Gnomad ASJ

AF:

0.736

Gnomad EAS

AF:

0.705

Gnomad SAS

AF:

0.443

Gnomad FIN

AF:

0.674

Gnomad MID

AF:

0.753

Gnomad NFE

AF:

0.708

Gnomad OTH

AF:

0.685

GnomAD4 exome

AF:

0.671

AC:

287

AN:

428

Hom.:

Cov.:

AF XY:

0.676

AC XY:

173

AN XY:

256

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.673

AC:

284

AN:

422

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.659

AC:

100213

AN:

152076

Hom.:

33367

Cov.:

AF XY:

0.655

AC XY:

48705

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.582

AC:

24106

AN:

41444

American (AMR)

AF:

0.663

AC:

10145

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.736

AC:

2551

AN:

3464

East Asian (EAS)

AF:

0.705

AC:

3648

AN:

5176

South Asian (SAS)

AF:

0.444

AC:

2141

AN:

4818

European-Finnish (FIN)

AF:

0.674

AC:

7128

AN:

10582

Middle Eastern (MID)

AF:

0.745

AC:

219

AN:

294

European-Non Finnish (NFE)

AF:

0.708

AC:

48140

AN:

67986

Other (OTH)

AF:

0.679

AC:

1432

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1788

3576

5363

7151

8939

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

796

1592

2388

3184

3980

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.683

Hom.:

14311

Bravo

AF:

0.661

Asia WGS

AF:

0.568

AC:

1974

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

(source)

DANN

Benign

0.75

PhyloP100

0.90

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over