chr6-89118336-T-G

Position:

• chr6-89118336-T-G

Variant summary

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

The XM_011535481.4(PM20D2):​c.-94+20666T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 152,032 control chromosomes in the GnomAD database, including 38,652 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 0.71 (38652 hom., cov: 34)
• Consequence: PM20D2 XM_011535481.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

Genes affected

PM20D2 (HGNC:21408): (peptidase M20 domain containing 2) Enables dipeptidase activity and identical protein binding activity. Acts upstream of or within proteolysis and regulation of cellular protein metabolic process. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PM20D2	XM_011535481.4	c.-94+20666T>G		intron_variant			XP_011533783.1
PM20D2	XM_047418220.1	c.-834+20666T>G		intron_variant			XP_047274176.1
PM20D2	XM_047418221.1	c.-144+20666T>G		intron_variant			XP_047274177.1
		n.89118336T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108211 AN: 151914 Hom.: 38643 Cov.: 34

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.712 AC: 108261 AN: 152032 Hom.: 38652 Cov.: 34 AF XY: 0.717 AC XY: 53306 AN XY: 74316

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.698

Alfa AF: 0.716 Hom.: 4858

Bravo AF: 0.703

Asia WGS AF: 0.766 AC: 2661 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.7
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs423516; hg19: chr6-89828055;