rs4707518

Variant names:

• chr6-89141287-A-C
• rs4707518
• XM_005248662.5:c.-94+846A>C

Variant summary

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

The ENST00000842482.1(ENSG00000309618):​n.1046A>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 0.362 in 152,068 control chromosomes in the GnomAD database, including 10,943 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 0.36 (10943 hom., cov: 32)
• Consequence: ENSG00000309618 ENST00000842482.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• Publications: 7 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842482.1. 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	ENST00000842482.1		n.1046A>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000309618	ENST00000842483.1		n.766A>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000288009	ENST00000657573.2		n.391+2460T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54923 AN: 151950 Hom.: 10890 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.362 AC: 55041 AN: 152068 Hom.: 10943 Cov.: 32 AF XY: 0.356 AC XY: 26452 AN XY: 74332

African (AFR) AF: 0.535 AC: 22188 AN: 41464

American (AMR) AF: 0.366 AC: 5594 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1334 AN: 5180

South Asian (SAS) AF: 0.241 AC: 1161 AN: 4820

European-Finnish (FIN) AF: 0.286 AC: 3020 AN: 10574

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19474 AN: 67982

Other (OTH) AF: 0.367 AC: 775 AN: 2110

Alfa AF: 0.344 Hom.: 1728

Bravo AF: 0.381

Asia WGS AF: 0.301 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.4
DANN	Benign	0.55
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs4707518; hg19: chr6-89851006;