chr5-71383799-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000415808.1(PMCHL2):​n.1526-1497G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: PMCHL2 ENST00000415808.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PMCHL2	NR_003922.1	n.1527-1497G>T		intron_variant	Intron 2 of 3
LINC02197	NR_134268.1	n.529-29876C>A		intron_variant	Intron 2 of 2
LINC02197	NR_134269.1	n.200+61846C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PMCHL2	ENST00000415808.1	n.1526-1497G>T		intron_variant	Intron 2 of 3	1
PMCHL2	ENST00000450213.6	n.1526-1497G>T		intron_variant	Intron 2 of 3	1
LINC02197	ENST00000517705.1	n.529-29876C>A		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.071
DANN	Benign	0.89

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;