12-6235220-C-G
Position:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000009180.10(CD9):c.349-9C>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000962 in 1,584,572 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0051 ( 7 hom., cov: 33)
Exomes 𝑓: 0.00052 ( 6 hom. )
Consequence
CD9
ENST00000009180.10 splice_polypyrimidine_tract, intron
ENST00000009180.10 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.008590
2
Clinical Significance
Conservation
PhyloP100: 0.217
Genes affected
CD9 (HGNC:1709): (CD9 molecule) This gene encodes a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Tetraspanins are cell surface glycoproteins with four transmembrane domains that form multimeric complexes with other cell surface proteins. The encoded protein functions in many cellular processes including differentiation, adhesion, and signal transduction, and expression of this gene plays a critical role in the suppression of cancer cell motility and metastasis. [provided by RefSeq, Jan 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 12-6235220-C-G is Benign according to our data. Variant chr12-6235220-C-G is described in ClinVar as [Benign]. Clinvar id is 722139.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00509 (776/152322) while in subpopulation AFR AF= 0.0171 (711/41566). AF 95% confidence interval is 0.0161. There are 7 homozygotes in gnomad4. There are 350 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD9 | NM_001769.4 | c.349-9C>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000009180.10 | NP_001760.1 | |||
LOC105369625 | XR_001748978.2 | n.412-11002G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD9 | ENST00000009180.10 | c.349-9C>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001769.4 | ENSP00000009180 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00510 AC: 776AN: 152204Hom.: 7 Cov.: 33
GnomAD3 genomes
AF:
AC:
776
AN:
152204
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00144 AC: 360AN: 250174Hom.: 1 AF XY: 0.00101 AC XY: 137AN XY: 135186
GnomAD3 exomes
AF:
AC:
360
AN:
250174
Hom.:
AF XY:
AC XY:
137
AN XY:
135186
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000522 AC: 748AN: 1432250Hom.: 6 Cov.: 27 AF XY: 0.000460 AC XY: 327AN XY: 710334
GnomAD4 exome
AF:
AC:
748
AN:
1432250
Hom.:
Cov.:
27
AF XY:
AC XY:
327
AN XY:
710334
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00509 AC: 776AN: 152322Hom.: 7 Cov.: 33 AF XY: 0.00470 AC XY: 350AN XY: 74498
GnomAD4 genome
AF:
AC:
776
AN:
152322
Hom.:
Cov.:
33
AF XY:
AC XY:
350
AN XY:
74498
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
5
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 18, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at