3-12545634-A-T

Variant names:

• chr3-12545634-A-T
• rs11706408
• NM_001378007.1:c.-89-3612T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001378007.1(MKRN2OS):​c.-89-3612T>A 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: 32)
• Consequence: MKRN2OS NM_001378007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 11 publications found

Genes affected

MKRN2OS (HGNC:40375): (MKRN2 opposite strand)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MKRN2OS	NM_001195279.2	c.-170T>A		upstream_gene_variant		ENST00000564146.4	NP_001182208.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MKRN2OS	ENST00000567514.1	n.304-2405T>A		intron_variant	Intron 1 of 5	5
MKRN2OS	ENST00000678164.1	n.1068-3612T>A		intron_variant	Intron 1 of 2
MKRN2OS	ENST00000564146.4	c.-170T>A		upstream_gene_variant		5	NM_001195279.2	ENSP00000455385.3
MKRN2OS	ENST00000561645.2	n.-170T>A		upstream_gene_variant		5		ENSP00000456723.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 664

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.80
PhyloP100		-0.40
PromoterAI		0.027	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11706408; hg19: chr3-12587133;