15-58816117-T-C

Position:

• chr15-58816117-T-C

Variant summary

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

The NM_001040450.3(MINDY2):​c.1123-5600T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,158 control chromosomes in the GnomAD database, including 5,524 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 0.26 (5524 hom., cov: 32)
• Consequence: MINDY2 NM_001040450.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

Genes affected

MINDY2 (HGNC:26954): (MINDY lysine 48 deubiquitinase 2) Enables cysteine-type peptidase activity and polyubiquitin modification-dependent protein binding activity. Predicted to be involved in protein K48-linked deubiquitination. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MINDY2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) 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
MINDY2	NM_001040450.3	c.1123-5600T>C		intron_variant		ENST00000559228.6	NP_001035540.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MINDY2	ENST00000559228.6	c.1123-5600T>C		intron_variant		2	NM_001040450.3	ENSP00000452885.1

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39087 AN: 152040 Hom.: 5522 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.257 AC: 39119 AN: 152158 Hom.: 5524 Cov.: 32 AF XY: 0.263 AC XY: 19587 AN XY: 74390

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.266

Alfa AF: 0.216 Hom.: 1733

Bravo AF: 0.269

Asia WGS AF: 0.419 AC: 1452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.34

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: rs574683; hg19: chr15-59108316;