dbSNP rs13163: SNPH:c.*2887A>G (chr20-1308941-A-G) – 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.*2887A>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 0.0383 in 152,398 control chromosomes in the GnomAD database, including 159 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 0.038 ( 159 hom., cov: 33)

Exomes 𝑓: 0.015 ( 0 hom. )

Consequence

SNPH
NM_001318234.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.34

Publications

10 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=-0.48).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNPH	NM_001318234.2 link	c.*2887A>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000381867.6	NP_001305163.1	O15079-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SNPH	ENST00000381867.6 link	c.*2887A>G	3_prime_UTR_variant	Exon 7 of 7	1	NM_001318234.2	ENSP00000371291.1	O15079-2
SNPH	ENST00000614659.1 link	c.*2887A>G	3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000479696.1	O15079-2
SNPH	ENST00000381873.7 link	c.*2887A>G	3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000371297.3	O15079-1

Frequencies

GnomAD3 genomes

AF:

0.0383

AC:

5831

AN:

152212

Hom.:

159

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00900

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.0330

Gnomad ASJ

AF:

0.107

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0648

Gnomad FIN

AF:

0.0277

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0555

Gnomad OTH

AF:

0.0483

GnomAD4 exome

AF:

0.0147

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0192

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

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:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0179

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0383

AC:

5831

AN:

152330

Hom.:

159

Cov.:

AF XY:

0.0380

AC XY:

2832

AN XY:

74482

show subpopulations

African (AFR)

AF:

0.00897

AC:

373

AN:

41574

American (AMR)

AF:

0.0330

AC:

505

AN:

15314

Ashkenazi Jewish (ASJ)

AF:

0.107

AC:

373

AN:

3470

East Asian (EAS)

AF:

0.000772

AC:

AN:

5184

South Asian (SAS)

AF:

0.0650

AC:

314

AN:

4828

European-Finnish (FIN)

AF:

0.0277

AC:

294

AN:

10622

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0555

AC:

3777

AN:

68018

Other (OTH)

AF:

0.0482

AC:

102

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

289

578

867

1156

1445

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

216

288

360

<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:

0.0560

Hom.:

154

Bravo

AF:

0.0374

Asia WGS

AF:

0.0320

AC:

110

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

(source)

DANN

Benign

0.77

PhyloP100

1.3

Mutation Taster

=100/0

polymorphism

(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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over