rs11240572

Variant names:

• chr1-205838885-C-A
• rs11240572
• NM_152491.5:c.1116+1367G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-205838885-C-A
• chr1-205838885-C-T

Variant summary

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

The NM_152491.5(PM20D1):​c.1116+1367G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0396 in 152,276 control chromosomes in the GnomAD database, including 287 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 0.040 (287 hom., cov: 32)
• Consequence: PM20D1 NM_152491.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 20 publications found

Genes affected

PM20D1 (HGNC:26518): (peptidase M20 domain containing 1) Enables hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides. Involved in several processes, including amide biosynthetic process; cellular amide catabolic process; and negative regulation of neuron death. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

PM20D1-AS1 (HGNC:27633): (PM20D1 antisense RNA 1)

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 (EAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PM20D1	NM_152491.5	c.1116+1367G>T		intron_variant	Intron 10 of 12	ENST00000367136.5	NP_689704.4
PM20D1	NR_135186.2	n.1114+1367G>T		intron_variant	Intron 9 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PM20D1	ENST00000367136.5	c.1116+1367G>T		intron_variant	Intron 10 of 12	1	NM_152491.5	ENSP00000356104.4

Frequencies

GnomAD3 genomes AF: 0.0395 AC: 6016 AN: 152158 Hom.: 284 Cov.: 32

Gnomad AFR AF: 0.00753

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0812

Gnomad ASJ AF: 0.0791

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0396 AC: 6032 AN: 152276 Hom.: 287 Cov.: 32 AF XY: 0.0423 AC XY: 3151 AN XY: 74474

African (AFR) AF: 0.00748 AC: 311 AN: 41568

American (AMR) AF: 0.0820 AC: 1254 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0791 AC: 274 AN: 3466

East Asian (EAS) AF: 0.177 AC: 918 AN: 5178

South Asian (SAS) AF: 0.127 AC: 614 AN: 4816

European-Finnish (FIN) AF: 0.0317 AC: 337 AN: 10624

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0324 AC: 2205 AN: 68008

Other (OTH) AF: 0.0421 AC: 89 AN: 2112

Alfa AF: 0.0366 Hom.: 121

Bravo AF: 0.0435

Asia WGS AF: 0.140 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.19
DANN	Benign	0.80
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11240572; hg19: chr1-205808013;