6-89118336-T-C

Variant names:

• chr6-89118336-T-C
• rs423516
• ENST00000842480.1:n.89+164T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000842480.1(ENSG00000309618):​n.89+164T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
• Consequence: ENSG00000309618 ENST00000842480.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 0 publications found

Genes affected

ENSG00000309618 (HGNC:):

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PM20D2	XM_011535481.4	c.-94+20666T>C		intron_variant	Intron 1 of 6		XP_011533783.1
PM20D2	XM_047418220.1	c.-834+20666T>C		intron_variant	Intron 1 of 6		XP_047274176.1
PM20D2	XM_047418221.1	c.-144+20666T>C		intron_variant	Intron 1 of 7		XP_047274177.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309618	ENST00000842480.1	n.89+164T>C		intron_variant	Intron 1 of 3
ENSG00000309618	ENST00000842481.1	n.80+164T>C		intron_variant	Intron 1 of 3
ENSG00000309618	ENST00000842482.1	n.81+164T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 34

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

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.45
PhyloP100		0.23
PromoterAI		0.18	Neutral

Splicing

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

Other links and lift over

dbSNP: rs423516; hg19: chr6-89828055;