5-71383799-G-A

Variant names:

• chr5-71383799-G-A
• rs13168712
• ENST00000415808.1:n.1526-1497G>A

Variant summary

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

The ENST00000415808.1(PMCHL2):​n.1526-1497G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,756 control chromosomes in the GnomAD database, including 23,420 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 0.51 (23420 hom., cov: 31)
• Consequence: PMCHL2 ENST00000415808.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895
• Publications: 21 publications found

Genes affected

PMCHL2 (HGNC:):

LINC02197 (HGNC:53063): (long intergenic non-protein coding RNA 2197)

PMCHL2 (HGNC:9111): (pro-melanin concentrating hormone like 2 (pseudogene)) Predicted to enable type 1 melanin-concentrating hormone receptor binding activity. Predicted to be involved in chemical synaptic transmission and signal transduction. Predicted to be located in synapse. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415808.1. 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
	PMCHL2	NR_003922.1		n.1527-1497G>A		intron	N/A
	LINC02197	NR_134268.1		n.529-29876C>T		intron	N/A
	LINC02197	NR_134269.1		n.200+61846C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PMCHL2	ENST00000415808.1	TSL:1	n.1526-1497G>A		intron	N/A
	PMCHL2	ENST00000450213.6	TSL:1	n.1526-1497G>A		intron	N/A
	LINC02197	ENST00000517705.1	TSL:1	n.529-29876C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77895 AN: 151638 Hom.: 23420 Cov.: 31

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.513 AC: 77883 AN: 151756 Hom.: 23420 Cov.: 31 AF XY: 0.522 AC XY: 38714 AN XY: 74144

African (AFR) AF: 0.183 AC: 7578 AN: 41404

American (AMR) AF: 0.595 AC: 9057 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3464

East Asian (EAS) AF: 0.838 AC: 4324 AN: 5158

South Asian (SAS) AF: 0.735 AC: 3532 AN: 4808

European-Finnish (FIN) AF: 0.675 AC: 7070 AN: 10472

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42867 AN: 67914

Other (OTH) AF: 0.506 AC: 1069 AN: 2112

Alfa AF: 0.596 Hom.: 77920

Bravo AF: 0.491

Asia WGS AF: 0.726 AC: 2513 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.088
DANN	Benign	0.92
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs13168712; hg19: chr5-70679626;