11-60171834-T-G

Variant summary

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

The NM_152852.3(MS4A6A):​c.*324A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 151,962 control chromosomes in the GnomAD database, including 25,145 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 0.57 ( 25145 hom., cov: 31)

Consequence

MS4A6A
NM_152852.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.291
Variant links:
Genes affected
MS4A6A (HGNC:13375): (membrane spanning 4-domains A6A) 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 11q12.1, among a cluster of family members. Alternative splicing of this gene results in several transcript variants that encode different protein isoforms. [provided by RefSeq, Oct 2011]

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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=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MS4A6ANM_152852.3 linkc.*324A>C 3_prime_UTR_variant Exon 8 of 8 NP_690591.1 Q9H2W1-1A0A024R554
MS4A6ANM_152851.2 linkc.*430A>C 3_prime_UTR_variant Exon 7 of 7 NP_690590.1 Q9H2W1-3
MS4A6AXM_005274177.4 linkc.*324A>C 3_prime_UTR_variant Exon 8 of 8 XP_005274234.1 E9PSA9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MS4A6AENST00000420732.6 linkc.*430A>C downstream_gene_variant 1 ENSP00000392921.2 Q9H2W1-3
MS4A6AENST00000529054.5 linkc.*324A>C downstream_gene_variant 5 ENSP00000435844.1 E9PSA9
MS4A6AENST00000530839.5 linkc.*324A>C downstream_gene_variant 2 ENSP00000436979.1 Q9H2W1-1

Frequencies

GnomAD3 genomes
AF:
0.572
AC:
86888
AN:
151846
Hom.:
25134
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.513
Gnomad AMI
AF:
0.574
Gnomad AMR
AF:
0.648
Gnomad ASJ
AF:
0.540
Gnomad EAS
AF:
0.629
Gnomad SAS
AF:
0.436
Gnomad FIN
AF:
0.711
Gnomad MID
AF:
0.446
Gnomad NFE
AF:
0.578
Gnomad OTH
AF:
0.544
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.572
AC:
86929
AN:
151962
Hom.:
25145
Cov.:
31
AF XY:
0.577
AC XY:
42861
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.512
Gnomad4 AMR
AF:
0.648
Gnomad4 ASJ
AF:
0.540
Gnomad4 EAS
AF:
0.629
Gnomad4 SAS
AF:
0.435
Gnomad4 FIN
AF:
0.711
Gnomad4 NFE
AF:
0.578
Gnomad4 OTH
AF:
0.545
Alfa
AF:
0.569
Hom.:
54282
Bravo
AF:
0.568
Asia WGS
AF:
0.527
AC:
1830
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.69
DANN
Benign
0.64

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: rs610932; hg19: chr11-59939307; COSMIC: COSV60616357; API