chr10-15860304-A-G

Variant names:

• chr10-15860304-A-G
• rs2297882
• ENST00000477891.1:n.195T>C

Variant summary

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

The ENST00000477891.1(MINDY3):​n.195T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 1,591,298 control chromosomes in the GnomAD database, including 63,952 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 0.33 (9030 hom., cov: 33)
  • Exomes 𝑓: 0.27 (54922 hom.)
• Consequence: MINDY3 ENST00000477891.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 14 publications found

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]

ENSG00000293799 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MINDY3	NM_024948.4	c.-5T>C		5_prime_UTR_variant	Exon 1 of 15	ENST00000277632.8	NP_079224.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MINDY3	ENST00000477891.1	n.195T>C		non_coding_transcript_exon_variant	Exon 1 of 14	1
MINDY3	ENST00000277632.8	c.-5T>C		5_prime_UTR_variant	Exon 1 of 15	1	NM_024948.4	ENSP00000277632.3
ENSG00000293799	ENST00000719107.1	n.276A>G		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50690 AN: 152042 Hom.: 9003 Cov.: 33

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.305

GnomAD2 exomes AF: 0.293 AC: 63916 AN: 218046 AF XY: 0.292

Gnomad AFR exome AF: 0.455

Gnomad AMR exome AF: 0.297

Gnomad ASJ exome AF: 0.280

Gnomad EAS exome AF: 0.191

Gnomad FIN exome AF: 0.361

Gnomad NFE exome AF: 0.275

Gnomad OTH exome AF: 0.282

GnomAD4 exome AF: 0.272 AC: 391299 AN: 1439138 Hom.: 54922 Cov.: 31 AF XY: 0.272 AC XY: 194461 AN XY: 713892

African (AFR) AF: 0.466 AC: 15473 AN: 33192

American (AMR) AF: 0.293 AC: 12212 AN: 41618

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 7134 AN: 25710

East Asian (EAS) AF: 0.191 AC: 7487 AN: 39098

South Asian (SAS) AF: 0.295 AC: 24528 AN: 83100

European-Finnish (FIN) AF: 0.364 AC: 18926 AN: 51936

Middle Eastern (MID) AF: 0.310 AC: 1769 AN: 5708

European-Non Finnish (NFE) AF: 0.261 AC: 287140 AN: 1099206

Other (OTH) AF: 0.279 AC: 16630 AN: 59570

GnomAD4 genome AF: 0.334 AC: 50755 AN: 152160 Hom.: 9030 Cov.: 33 AF XY: 0.338 AC XY: 25107 AN XY: 74388

African (AFR) AF: 0.460 AC: 19092 AN: 41516

American (AMR) AF: 0.317 AC: 4847 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 954 AN: 3470

East Asian (EAS) AF: 0.188 AC: 971 AN: 5172

South Asian (SAS) AF: 0.277 AC: 1336 AN: 4824

European-Finnish (FIN) AF: 0.371 AC: 3927 AN: 10594

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18686 AN: 67980

Other (OTH) AF: 0.303 AC: 642 AN: 2116

Alfa AF: 0.298 Hom.: 6528

Bravo AF: 0.336

Asia WGS AF: 0.246 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	16
DANN	Benign	0.72
PhyloP100		1.2
PromoterAI		-0.040	Neutral
Mutation Taster		=296/4	polymorphism (auto)

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: rs2297882; hg19: chr10-15902303; COSMIC: COSV53220020;