3-150892138-T-C

Variant names:

• chr3-150892138-T-C
• rs628383
• NM_001351281.2:c.522-1035A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001351281.2(MINDY4B):​c.522-1035A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,208 control chromosomes in the GnomAD database, including 47,345 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 0.78 (47345 hom., cov: 33)
• Consequence: MINDY4B NM_001351281.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 4 publications found

Genes affected

MINDY4B (HGNC:35475): (MINDY family member 4B) Predicted to enable Lys48-specific deubiquitinase activity. Predicted to be involved in protein K48-linked deubiquitination. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000260234 (HGNC:):

SIAH2-AS1 (HGNC:40526): (SIAH2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001351281.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MINDY4B	NM_001351281.2	MANE Select	c.522-1035A>G		intron	N/A	NP_001338210.2	A8MYZ0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MINDY4B	ENST00000465419.7	TSL:5 MANE Select	c.522-1035A>G		intron	N/A	ENSP00000491923.1	A8MYZ0
	ENSG00000260234	ENST00000562308.5	TSL:1	n.*169-1035A>G		intron	N/A	ENSP00000457487.1	H3BU62
	ENSG00000260234	ENST00000565169.1	TSL:1	n.*77-988A>G		intron	N/A	ENSP00000455583.1	H3BQ33

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118719 AN: 152090 Hom.: 47294 Cov.: 33

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.780

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.781 AC: 118822 AN: 152208 Hom.: 47345 Cov.: 33 AF XY: 0.778 AC XY: 57869 AN XY: 74418

African (AFR) AF: 0.943 AC: 39203 AN: 41556

American (AMR) AF: 0.670 AC: 10242 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2784 AN: 3472

East Asian (EAS) AF: 0.594 AC: 3069 AN: 5170

South Asian (SAS) AF: 0.798 AC: 3845 AN: 4820

European-Finnish (FIN) AF: 0.729 AC: 7717 AN: 10590

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49459 AN: 67992

Other (OTH) AF: 0.779 AC: 1642 AN: 2108

Alfa AF: 0.747 Hom.: 61354

Bravo AF: 0.781

Asia WGS AF: 0.711 AC: 2474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.025
DANN	Benign	0.55
PhyloP100		-2.1

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

Other links and lift over

dbSNP: rs628383; hg19: chr3-150609925;