6-89118336-T-G

Variant names:

• chr6-89118336-T-G
• rs423516
• XM_011535481.4:c.-94+20666T>G

Variant summary

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

The ENST00000842480.1(ENSG00000309618):​n.89+164T>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: ENSG00000309618 ENST00000842480.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 3 publications found

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]

ENSG00000309618 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842480.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309618	ENST00000842480.1		n.89+164T>G		intron	N/A
	ENSG00000309618	ENST00000842481.1		n.80+164T>G		intron	N/A
	ENSG00000309618	ENST00000842482.1		n.81+164T>G		intron	N/A

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

African (AFR) AF: 0.706 AC: 29289 AN: 41514

American (AMR) AF: 0.672 AC: 10279 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2288 AN: 3470

East Asian (EAS) AF: 0.798 AC: 4107 AN: 5146

South Asian (SAS) AF: 0.794 AC: 3829 AN: 4824

European-Finnish (FIN) AF: 0.716 AC: 7591 AN: 10602

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48523 AN: 67884

Other (OTH) AF: 0.698 AC: 1468 AN: 2102

Alfa AF: 0.716 Hom.: 5046

Bravo AF: 0.703

Asia WGS AF: 0.766 AC: 2661 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.7
DANN	Benign	0.18
PhyloP100		0.23
PromoterAI		-0.030	Neutral

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs423516;

hg19: chr6-89828055;