rs185930615

Variant names:

• chr20-40686360-G-A
• rs185930615
• NM_005461.5:c.*1519C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-40686360-G-A
• chr20-40686360-G-C
• chr20-40686360-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005461.5(MAFB):​c.*1519C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 110,872 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.000018 (0 hom.)
• Consequence: MAFB NM_005461.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAFB	NM_005461.5	c.*1519C>T		3_prime_UTR_variant	Exon 1 of 1	ENST00000373313.3	NP_005452.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAFB	ENST00000373313.3	c.*1519C>T		3_prime_UTR_variant	Exon 1 of 1	6	NM_005461.5	ENSP00000362410.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.0000180 AC: 2 AN: 110872 Hom.: 0 Cov.: 0 AF XY: 0.0000188 AC XY: 1 AN XY: 53130

African (AFR) AF: 0.00 AC: 0 AN: 4916

American (AMR) AF: 0.00 AC: 0 AN: 3284

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5912

East Asian (EAS) AF: 0.000163 AC: 2 AN: 12246

South Asian (SAS) AF: 0.00 AC: 0 AN: 990

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2812

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 662

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 71464

Other (OTH) AF: 0.00 AC: 0 AN: 8586

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.65
PhyloP100		0.29

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

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Other links and lift over

dbSNP: rs185930615; hg19: chr20-39315000;