chr11-60251677-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000649552.2(MS4A4A):c.60-40548C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 152,034 control chromosomes in the GnomAD database, including 31,034 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 0.64 ( 31034 hom., cov: 31)
Consequence
MS4A4A
ENST00000649552.2 intron
ENST00000649552.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0110
Publications
17 publications found
Genes affected
MS4A4A (HGNC:13371): (membrane spanning 4-domains A4A) This gene encodes a member of the membrane-spanning 4A gene family. Members of this nascent protein family are characterized by common structural features, similar intron/exon splice boundaries, and display unique expression patterns in hematopoietic cells and nonlymphoid tissues. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
Genome browser will be placed here
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=-0.62).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MS4A4A | ENST00000649552.2 | c.60-40548C>T | intron_variant | Intron 2 of 7 | ENSP00000497952.2 | |||||
MS4A4A | ENST00000679553.1 | c.60-40548C>T | intron_variant | Intron 1 of 6 | ENSP00000505712.1 | |||||
MS4A4A | ENST00000681288.1 | c.60-40548C>T | intron_variant | Intron 2 of 7 | ENSP00000505714.1 |
Frequencies
GnomAD3 genomes AF: 0.636 AC: 96556AN: 151916Hom.: 31020 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
96556
AN:
151916
Hom.:
Cov.:
31
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.635 AC: 96614AN: 152034Hom.: 31034 Cov.: 31 AF XY: 0.638 AC XY: 47441AN XY: 74304 show subpopulations
GnomAD4 genome
AF:
AC:
96614
AN:
152034
Hom.:
Cov.:
31
AF XY:
AC XY:
47441
AN XY:
74304
show subpopulations
African (AFR)
AF:
AC:
29448
AN:
41436
American (AMR)
AF:
AC:
8983
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
2125
AN:
3470
East Asian (EAS)
AF:
AC:
3491
AN:
5152
South Asian (SAS)
AF:
AC:
2393
AN:
4812
European-Finnish (FIN)
AF:
AC:
7738
AN:
10562
Middle Eastern (MID)
AF:
AC:
157
AN:
294
European-Non Finnish (NFE)
AF:
AC:
40433
AN:
68010
Other (OTH)
AF:
AC:
1252
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1825
3650
5474
7299
9124
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
778
1556
2334
3112
3890
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2122
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.