dbSNP rs3803947: SNPH:c.*2268G>A (chr20-1308322-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_001318234.2(SNPH):c.*2268G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,442 control chromosomes in the GnomAD database, including 17,360 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 0.47 ( 17337 hom., cov: 33)

Exomes 𝑓: 0.37 ( 23 hom. )

Consequence

SNPH
NM_001318234.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.162

Publications

7 publications found

Variant links:

Genes affected

SNPH (HGNC:15931): (syntaphilin) Syntaxin-1, synaptobrevin/VAMP, and SNAP25 interact to form the SNARE complex, which is required for synaptic vesicle docking and fusion. The protein encoded by this gene is membrane-associated and inhibits SNARE complex formation by binding free syntaxin-1. Expression of this gene appears to be brain-specific. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

SNPH links:

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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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318234.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SNPH	NM_001318234.2	MANE Select	c.*2268G>A	3_prime_UTR	Exon 7 of 7	NP_001305163.1
SNPH	NM_001439257.1		c.*2268G>A	3_prime_UTR	Exon 7 of 7	NP_001426186.1
SNPH	NM_001439258.1		c.*2268G>A	3_prime_UTR	Exon 6 of 6	NP_001426187.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SNPH	ENST00000381867.6	TSL:1 MANE Select	c.*2268G>A	3_prime_UTR	Exon 7 of 7	ENSP00000371291.1
SNPH	ENST00000614659.1	TSL:1	c.*2268G>A	3_prime_UTR	Exon 4 of 4	ENSP00000479696.1
SNPH	ENST00000381873.7	TSL:1	c.*2268G>A	3_prime_UTR	Exon 6 of 6	ENSP00000371297.3

Frequencies

GnomAD3 genomes

AF:

0.466

AC:

70865

AN:

152012

Hom.:

17316

Cov.:

show subpopulations

Gnomad AFR

AF:

0.580

Gnomad AMI

AF:

0.395

Gnomad AMR

AF:

0.429

Gnomad ASJ

AF:

0.469

Gnomad EAS

AF:

0.0901

Gnomad SAS

AF:

0.302

Gnomad FIN

AF:

0.373

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.461

Gnomad OTH

AF:

0.460

GnomAD4 exome

AF:

0.372

AC:

116

AN:

312

Hom.:

Cov.:

AF XY:

0.376

AC XY:

AN XY:

234

show subpopulations

African (AFR)

AF:

0.667

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.125

AC:

AN:

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.384

AC:

AN:

258

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

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:

0.466

AC:

70924

AN:

152130

Hom.:

17337

Cov.:

AF XY:

0.455

AC XY:

33841

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.580

AC:

24079

AN:

41522

American (AMR)

AF:

0.429

AC:

6550

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.469

AC:

1626

AN:

3466

East Asian (EAS)

AF:

0.0895

AC:

463

AN:

5172

South Asian (SAS)

AF:

0.303

AC:

1459

AN:

4822

European-Finnish (FIN)

AF:

0.373

AC:

3954

AN:

10588

Middle Eastern (MID)

AF:

0.510

AC:

150

AN:

294

European-Non Finnish (NFE)

AF:

0.461

AC:

31324

AN:

67968

Other (OTH)

AF:

0.455

AC:

960

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

1876

3752

5628

7504

9380

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

622

1244

1866

2488

3110

<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:

0.463

Hom.:

2085

Bravo

AF:

0.474

Asia WGS

AF:

0.231

AC:

803

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.4

(source)

DANN

Benign

0.87

PhyloP100

0.16

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