10-92419591-G-T

Variant summary

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

The NR_038243.2(MARK2P9):n.931G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 152,142 control chromosomes in the GnomAD database, including 24,182 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 0.55 (24168 hom., cov: 31)
  • Exomes 𝑓: 0.41 (14 hom.)
• Consequence: MARK2P9 NR_038243.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

Genes affected

MARK2P9 (HGNC:39800): (MARK2 pseudogene 9)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MARK2P9	NR_038243.2	n.931G>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MARK2P9	ENST00000430958.1	n.925G>T		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82872 AN: 151908 Hom.: 24131 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.506

GnomAD4 exome AF: 0.414 AC: 48 AN: 116 Hom.: 14 Cov.: 0 AF XY: 0.384 AC XY: 33 AN XY: 86

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.600

Gnomad4 NFE exome AF: 0.337

Gnomad4 OTH exome AF: 0.700

GnomAD4 genome AF: 0.546 AC: 82970 AN: 152026 Hom.: 24168 Cov.: 31 AF XY: 0.551 AC XY: 40944 AN XY: 74308

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.506

Alfa AF: 0.399 Hom.: 2127

Bravo AF: 0.558

Asia WGS AF: 0.750 AC: 2608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	0.77
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs967878; hg19: chr10-94179348;