20-40686286-GA-G

Position:

• chr20-40686286-GA-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_005461.5(MAFB):​c.*1592delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 207,354 control chromosomes in the GnomAD database, including 10,973 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.30 (9435 hom., cov: 22)
  • Exomes 𝑓: 0.21 (1538 hom.)
• Consequence: MAFB NM_005461.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.04

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 20-40686286-GA-G is Benign according to our data. Variant chr20-40686286-GA-G is described in ClinVar as [Benign]. Clinvar id is 338380.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAFB	NM_005461.5	c.*1592delT		3_prime_UTR_variant	1/1	ENST00000373313.3	NP_005452.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAFB	ENST00000373313	c.*1592delT		3_prime_UTR_variant	1/1		NM_005461.5	ENSP00000362410.2

Frequencies

GnomAD3 genomes AF: 0.302 AC: 44671 AN: 147836 Hom.: 9409 Cov.: 22

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.265

GnomAD4 exome AF: 0.215 AC: 12770 AN: 59414 Hom.: 1538 Cov.: 0 AF XY: 0.211 AC XY: 5867 AN XY: 27816

Gnomad4 AFR exome AF: 0.565

Gnomad4 AMR exome AF: 0.209

Gnomad4 ASJ exome AF: 0.150

Gnomad4 EAS exome AF: 0.372

Gnomad4 SAS exome AF: 0.288

Gnomad4 FIN exome AF: 0.141

Gnomad4 NFE exome AF: 0.158

Gnomad4 OTH exome AF: 0.229

GnomAD4 genome AF: 0.302 AC: 44738 AN: 147940 Hom.: 9435 Cov.: 22 AF XY: 0.305 AC XY: 21953 AN XY: 71952

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.265

Bravo AF: 0.315

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Multicentric carpo-tarsal osteolysis with or without nephropathy Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs3215567; hg19: chr20-39314926;