rs12669187

Positions:

• chr7-30875863-G-A

Variant summary

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

The NM_032222.3(MINDY4):​c.1971+207G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0714 in 152,254 control chromosomes in the GnomAD database, including 631 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 0.071 (631 hom., cov: 32)
• Consequence: MINDY4 NM_032222.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

Genes affected

MINDY4 (HGNC:21916): (MINDY lysine 48 deubiquitinase 4) Predicted to enable Lys48-specific deubiquitinase activity. Predicted to be involved in protein K48-linked deubiquitination. [provided by Alliance of Genome Resources, Apr 2022]

INMT-MINDY4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MINDY4	NM_032222.3	c.1971+207G>A		intron_variant		ENST00000265299.6
INMT-MINDY4	NR_037598.1	n.2500+207G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MINDY4	ENST00000265299.6	c.1971+207G>A		intron_variant		1	NM_032222.3	P1
MINDY4	ENST00000409881.1	n.1804+207G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0712 AC: 10833 AN: 152136 Hom.: 622 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0931

Gnomad FIN AF: 0.0433

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0355

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0714 AC: 10875 AN: 152254 Hom.: 631 Cov.: 32 AF XY: 0.0719 AC XY: 5351 AN XY: 74460

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.0311

Gnomad4 ASJ AF: 0.0467

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0932

Gnomad4 FIN AF: 0.0433

Gnomad4 NFE AF: 0.0355

Gnomad4 OTH AF: 0.0625

Alfa AF: 0.0409 Hom.: 199

Bravo AF: 0.0725

Asia WGS AF: 0.107 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0090
DANN	Benign	0.57

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: rs12669187; hg19: chr7-30915478;