rs10795321

Positions:

• chr10-15819276-C-G

Variant summary

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

The NM_024948.4(MINDY3):​c.802-2361G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,014 control chromosomes in the GnomAD database, including 13,424 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 0.38 (13424 hom., cov: 32)
• Consequence: MINDY3 NM_024948.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

Genes affected

MINDY3 (HGNC:23578): (MINDY lysine 48 deubiquitinase 3) The protein encoded by this gene contains a caspase-associated recruitment domain and may function in apoptosis. It has been identified as a tumor suppressor in lung and gastric cancers, and a polymorphism in the gene may be associated with gastric cancer risk. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2015]

MINDY3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MINDY3	NM_024948.4	c.802-2361G>C		intron_variant		ENST00000277632.8	NP_079224.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MINDY3	ENST00000277632.8	c.802-2361G>C		intron_variant		1	NM_024948.4	ENSP00000277632.3
MINDY3	ENST00000477891.1	n.949-2361G>C		intron_variant		1
MINDY3	ENST00000418767.5	c.322-2361G>C		intron_variant		3		ENSP00000388661.1
MINDY3	ENST00000436829.1	c.361-2361G>C		intron_variant		5		ENSP00000389883.1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58112 AN: 151896 Hom.: 13382 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.383 AC: 58199 AN: 152014 Hom.: 13424 Cov.: 32 AF XY: 0.382 AC XY: 28382 AN XY: 74286

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.342

Alfa AF: 0.345 Hom.: 1338

Bravo AF: 0.395

Asia WGS AF: 0.246 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs10795321; hg19: chr10-15861275;