Genetic Variant SNAI1:c.*514C>T (chr20-49988570-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_005985.4(SNAI1):c.*514C>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 0.0882 in 152,846 control chromosomes in the GnomAD database, including 700 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 0.088 ( 696 hom., cov: 32)

Exomes 𝑓: 0.076 ( 4 hom. )

Consequence

SNAI1
NM_005985.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.77

Publications

16 publications found

Variant links:

Genes affected

SNAI1 (HGNC:11128): (snail family transcriptional repressor 1) The Drosophila embryonic protein snail is a zinc finger transcriptional repressor which downregulates the expression of ectodermal genes within the mesoderm. The nuclear protein encoded by this gene is structurally similar to the Drosophila snail protein, and is also thought to be critical for mesoderm formation in the developing embryo. At least two variants of a similar processed pseudogene have been found on chromosome 2. [provided by RefSeq, Jul 2008]

SNAI1 Gene-Disease associations (from GenCC):

congenital heart disease
Inheritance: AD Classification: LIMITED Submitted by: ClinGen

SNAI1 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=-0.72).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005985.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNAI1	NM_005985.4	MANE Select	c.*514C>T		3_prime_UTR	Exon 3 of 3	NP_005976.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNAI1	ENST00000244050.3	TSL:1 MANE Select	c.*514C>T		3_prime_UTR	Exon 3 of 3	ENSP00000244050.2	O95863

Frequencies

GnomAD3 genomes

AF:

0.0883

AC:

13421

AN:

152072

Hom.:

693

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.0286

Gnomad AMR

AF:

0.0570

Gnomad ASJ

AF:

0.0876

Gnomad EAS

AF:

0.0354

Gnomad SAS

AF:

0.0386

Gnomad FIN

AF:

0.0743

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0727

Gnomad OTH

AF:

0.0805

GnomAD4 exome

AF:

0.0760

AC:

AN:

658

Hom.:

Cov.:

AF XY:

0.0924

AC XY:

AN XY:

368

show subpopulations

African (AFR)

AF:

0.333

AC:

AN:

American (AMR)

AF:

0.0278

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

AN:

East Asian (EAS)

AF:

0.0833

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.0943

AC:

AN:

244

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0592

AC:

AN:

304

Other (OTH)

AF:

0.111

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.533

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0883

AC:

13437

AN:

152188

Hom.:

696

Cov.:

AF XY:

0.0868

AC XY:

6461

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.143

AC:

5940

AN:

41524

American (AMR)

AF:

0.0570

AC:

872

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0876

AC:

304

AN:

3472

East Asian (EAS)

AF:

0.0355

AC:

183

AN:

5156

South Asian (SAS)

AF:

0.0391

AC:

188

AN:

4812

European-Finnish (FIN)

AF:

0.0743

AC:

788

AN:

10608

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0727

AC:

4944

AN:

68008

Other (OTH)

AF:

0.0796

AC:

168

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

629

1258

1887

2516

3145

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

150

300

450

600

750

<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:

0.0733

Hom.:

806

Bravo

AF:

0.0898

Asia WGS

AF:

0.0380

AC:

130

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

(source)

DANN

Benign

0.69

PhyloP100

1.8

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over