chr9-136377295-G-A

Variant summary

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

The NM_003086.4(SNAPC4):​c.4284+248C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,150 control chromosomes in the GnomAD database, including 11,285 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 0.38 ( 11285 hom., cov: 34)

Consequence

SNAPC4
NM_003086.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.27
Variant links:
Genes affected
SNAPC4 (HGNC:11137): (small nuclear RNA activating complex polypeptide 4) This gene encodes the largest subunit of the small nuclear RNA-activating protein (SNAP) complex. The encoded protein contains a Myb DNA-binding domain, and is essential for RNA polymerase II and III polymerase transcription from small nuclear RNA promoters. A mutation in this gene is associated with ankylosing spondylitis. [provided by RefSeq, Jul 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SNAPC4NM_003086.4 linkuse as main transcriptc.4284+248C>T intron_variant ENST00000684778.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SNAPC4ENST00000684778.1 linkuse as main transcriptc.4284+248C>T intron_variant NM_003086.4 P1
SNAPC4ENST00000298532.2 linkuse as main transcriptc.4284+248C>T intron_variant 1 P1
SNAPC4ENST00000637388.2 linkuse as main transcriptc.4284+248C>T intron_variant 5 P1
SNAPC4ENST00000689006.1 linkuse as main transcriptc.*3497+248C>T intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.378
AC:
57437
AN:
152032
Hom.:
11268
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.287
Gnomad AMI
AF:
0.414
Gnomad AMR
AF:
0.471
Gnomad ASJ
AF:
0.355
Gnomad EAS
AF:
0.301
Gnomad SAS
AF:
0.328
Gnomad FIN
AF:
0.413
Gnomad MID
AF:
0.199
Gnomad NFE
AF:
0.418
Gnomad OTH
AF:
0.351
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.378
AC:
57504
AN:
152150
Hom.:
11285
Cov.:
34
AF XY:
0.376
AC XY:
27988
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.287
Gnomad4 AMR
AF:
0.472
Gnomad4 ASJ
AF:
0.355
Gnomad4 EAS
AF:
0.301
Gnomad4 SAS
AF:
0.328
Gnomad4 FIN
AF:
0.413
Gnomad4 NFE
AF:
0.418
Gnomad4 OTH
AF:
0.353
Alfa
AF:
0.402
Hom.:
2060
Bravo
AF:
0.375
Asia WGS
AF:
0.375
AC:
1305
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.22
DANN
Benign
0.44

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: rs11794847; hg19: chr9-139271747; COSMIC: COSV53731475; COSMIC: COSV53731475; API