3-150870395-A-G

Position:

• chr3-150870395-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001351281.2(MINDY4B):​c.*650T>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 0.484 in 152,086 control chromosomes in the GnomAD database, including 18,854 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 0.48 (18854 hom., cov: 32)
• Consequence: MINDY4B NM_001351281.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

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]

SIAH2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MINDY4B	NM_001351281.2	c.*650T>C		3_prime_UTR_variant	12/12	ENST00000465419.7	NP_001338210.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MINDY4B	ENST00000465419.7	c.*650T>C		3_prime_UTR_variant	12/12	5	NM_001351281.2	ENSP00000491923.1
SIAH2-AS1	ENST00000663257.1	n.570A>G		splice_region_variant, non_coding_transcript_exon_variant	3/3
CLRN1-AS1	ENST00000476886.5	n.123+17789A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73445 AN: 151968 Hom.: 18813 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.484 AC: 73538 AN: 152086 Hom.: 18854 Cov.: 32 AF XY: 0.482 AC XY: 35836 AN XY: 74332

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.455

Alfa AF: 0.385 Hom.: 2506

Bravo AF: 0.484

Asia WGS AF: 0.504 AC: 1751 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.21
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17283761; hg19: chr3-150588182;