6-89143977-A-T

Variant names:

• chr6-89143977-A-T
• rs10223547
• ENST00000842480.1:n.922A>T

Variant summary

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

The ENST00000842480.1(ENSG00000309618):​n.922A>T 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 0.267 in 152,178 control chromosomes in the GnomAD database, including 5,533 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 0.27 (5533 hom., cov: 33)
• Consequence: ENSG00000309618 ENST00000842480.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 1 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.313 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309618	ENST00000842480.1		n.922A>T		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000288009	ENST00000657573.2		n.305-144T>A		intron	N/A
	ENSG00000288009	ENST00000664569.1		n.247-144T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40578 AN: 152060 Hom.: 5516 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.267 AC: 40637 AN: 152178 Hom.: 5533 Cov.: 33 AF XY: 0.261 AC XY: 19451 AN XY: 74408

African (AFR) AF: 0.262 AC: 10877 AN: 41504

American (AMR) AF: 0.321 AC: 4902 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1134 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1055 AN: 5182

South Asian (SAS) AF: 0.206 AC: 995 AN: 4824

European-Finnish (FIN) AF: 0.229 AC: 2427 AN: 10588

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18335 AN: 67998

Other (OTH) AF: 0.282 AC: 595 AN: 2112

Alfa AF: 0.258 Hom.: 681

Bravo AF: 0.278

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.77
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10223547; hg19: chr6-89853696;