chr20-40685871-A-T

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_005461.5(MAFB):​c.*2008T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 179,978 control chromosomes in the GnomAD database, including 1,118 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 958 hom., cov: 33)
Exomes 𝑓: 0.10 ( 160 hom. )

Consequence

MAFB
NM_005461.5 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.24
Variant links:
Genes affected
MAFB (HGNC:6408): (MAF bZIP transcription factor B) The protein encoded by this gene is a basic leucine zipper (bZIP) transcription factor that plays an important role in the regulation of lineage-specific hematopoiesis. The encoded nuclear protein represses ETS1-mediated transcription of erythroid-specific genes in myeloid cells. This gene contains no introns. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
Variant 20-40685871-A-T is Benign according to our data. Variant chr20-40685871-A-T is described in ClinVar as [Benign]. Clinvar id is 338372.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MAFBNM_005461.5 linkuse as main transcriptc.*2008T>A 3_prime_UTR_variant 1/1 ENST00000373313.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MAFBENST00000373313.3 linkuse as main transcriptc.*2008T>A 3_prime_UTR_variant 1/1 NM_005461.5 P1

Frequencies

GnomAD3 genomes
AF:
0.102
AC:
15471
AN:
152154
Hom.:
958
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0301
Gnomad AMI
AF:
0.109
Gnomad AMR
AF:
0.106
Gnomad ASJ
AF:
0.117
Gnomad EAS
AF:
0.0198
Gnomad SAS
AF:
0.107
Gnomad FIN
AF:
0.143
Gnomad MID
AF:
0.180
Gnomad NFE
AF:
0.142
Gnomad OTH
AF:
0.108
GnomAD4 exome
AF:
0.100
AC:
2782
AN:
27706
Hom.:
160
Cov.:
0
AF XY:
0.102
AC XY:
1305
AN XY:
12778
show subpopulations
Gnomad4 AFR exome
AF:
0.0280
Gnomad4 AMR exome
AF:
0.0761
Gnomad4 ASJ exome
AF:
0.102
Gnomad4 EAS exome
AF:
0.0106
Gnomad4 SAS exome
AF:
0.0833
Gnomad4 FIN exome
AF:
0.138
Gnomad4 NFE exome
AF:
0.136
Gnomad4 OTH exome
AF:
0.107
GnomAD4 genome
AF:
0.102
AC:
15464
AN:
152272
Hom.:
958
Cov.:
33
AF XY:
0.103
AC XY:
7684
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.0300
Gnomad4 AMR
AF:
0.106
Gnomad4 ASJ
AF:
0.117
Gnomad4 EAS
AF:
0.0199
Gnomad4 SAS
AF:
0.107
Gnomad4 FIN
AF:
0.143
Gnomad4 NFE
AF:
0.142
Gnomad4 OTH
AF:
0.107
Alfa
AF:
0.114
Hom.:
144
Bravo
AF:
0.0939
Asia WGS
AF:
0.0590
AC:
206
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Multicentric carpo-tarsal osteolysis with or without nephropathy Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.42
CADD
Benign
15
DANN
Benign
0.76

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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: rs56049320; hg19: chr20-39314511; API