rs17155019
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_152866.3(MS4A1):c.-171C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00846 in 753,748 control chromosomes in the GnomAD database, including 269 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.011 ( 77 hom., cov: 32)
Exomes 𝑓: 0.0078 ( 192 hom. )
Consequence
MS4A1
NM_152866.3 5_prime_UTR
NM_152866.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.130
Genes affected
MS4A1 (HGNC:7315): (membrane spanning 4-domains A1) This gene encodes a member of the membrane-spanning 4A gene family. Members of this nascent protein family are characterized by common structural features and similar intron/exon splice boundaries and display unique expression patterns among hematopoietic cells and nonlymphoid tissues. This gene encodes a B-lymphocyte surface molecule which plays a role in the development and differentiation of B-cells into plasma cells. This family member is localized to 11q12, among a cluster of family members. Alternative splicing of this gene results in two transcript variants which encode the same protein. [provided by RefSeq, Jul 2008]
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=-0.83).
BP6
?
Variant 11-60462204-C-T is Benign according to our data. Variant chr11-60462204-C-T is described in ClinVar as [Benign]. Clinvar id is 1229170.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0827 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MS4A1 | NM_152866.3 | c.-171C>T | 5_prime_UTR_variant | 3/8 | ENST00000345732.9 | ||
MS4A1 | NM_152867.2 | c.-171C>T | 5_prime_UTR_variant | 2/7 | |||
MS4A1 | NM_021950.4 | c.-16-155C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MS4A1 | ENST00000345732.9 | c.-171C>T | 5_prime_UTR_variant | 3/8 | 1 | NM_152866.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0109 AC: 1654AN: 152130Hom.: 77 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1654
AN:
152130
Hom.:
Cov.:
32
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: 0.0202 AC: 2862AN: 141792Hom.: 121 AF XY: 0.0164 AC XY: 1258AN XY: 76586
GnomAD3 exomes
AF:
AC:
2862
AN:
141792
Hom.:
AF XY:
AC XY:
1258
AN XY:
76586
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: 0.00785 AC: 4721AN: 601500Hom.: 192 Cov.: 8 AF XY: 0.00669 AC XY: 2156AN XY: 322240
GnomAD4 exome
AF:
AC:
4721
AN:
601500
Hom.:
Cov.:
8
AF XY:
AC XY:
2156
AN XY:
322240
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: 0.0109 AC: 1659AN: 152248Hom.: 77 Cov.: 32 AF XY: 0.0129 AC XY: 964AN XY: 74440
GnomAD4 genome
?
AF:
AC:
1659
AN:
152248
Hom.:
Cov.:
32
AF XY:
AC XY:
964
AN XY:
74440
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:
52
AN:
3478
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 | GeneDx | Jun 20, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at