rs1373061

Variant summary

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

The ENST00000532756.1(MS4A6E):​c.*162+17246A>C variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.92 in 152,240 control chromosomes in the GnomAD database, including 65,198 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 0.92 ( 65198 hom., cov: 32)

Consequence

MS4A6E
ENST00000532756.1 intron, NMD_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0360
Variant links:
Genes affected
MS4A6E (HGNC:14285): (membrane spanning 4-domains A6E) 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. The gene encoding this protein is localized to 11q12.3, among a cluster of family members. [provided by RefSeq, Jul 2008]

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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=-0.99).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MS4A6EENST00000532756.1 linkuse as main transcriptc.*162+17246A>C intron_variant, NMD_transcript_variant 4 ENSP00000432963

Frequencies

GnomAD3 genomes
AF:
0.920
AC:
140015
AN:
152122
Hom.:
65167
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.773
Gnomad AMI
AF:
0.985
Gnomad AMR
AF:
0.889
Gnomad ASJ
AF:
0.994
Gnomad EAS
AF:
0.893
Gnomad SAS
AF:
0.965
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
0.987
Gnomad NFE
AF:
0.998
Gnomad OTH
AF:
0.933
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.920
AC:
140100
AN:
152240
Hom.:
65198
Cov.:
32
AF XY:
0.919
AC XY:
68430
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.773
Gnomad4 AMR
AF:
0.889
Gnomad4 ASJ
AF:
0.994
Gnomad4 EAS
AF:
0.893
Gnomad4 SAS
AF:
0.965
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
0.998
Gnomad4 OTH
AF:
0.933
Alfa
AF:
0.971
Hom.:
14307
Bravo
AF:
0.907
Asia WGS
AF:
0.919
AC:
3199
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
1.2
DANN
Benign
0.77

Splicing

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: rs1373061; hg19: chr11-60125647; API