rs13168712

Positions:

• chr5-71383799-G-A
• chr5-71383799-G-C
• chr5-71383799-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_003922.1(PMCHL2):​n.1527-1497G>A variant causes a intron, non coding transcript 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 NR_003922.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895

Genes affected

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]

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PMCHL2	NR_003922.1	n.1527-1497G>A		intron_variant, non_coding_transcript_variant
LINC02197	NR_134269.1	n.200+61846C>T		intron_variant, non_coding_transcript_variant
LINC02197	NR_134268.1	n.529-29876C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PMCHL2	ENST00000415808.1	n.1526-1497G>A		intron_variant, non_coding_transcript_variant		1
LINC02197	ENST00000671145.1	n.217-29876C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.506

Alfa AF: 0.609 Hom.: 34255

Bravo AF: 0.491

Asia WGS AF: 0.726 AC: 2513 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13168712; hg19: chr5-70679626;