rs2209972

Positions:

• chr10-92419271-C-T

Variant summary

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

The NR_038243.2(MARK2P9):​n.611C>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 0.332 in 152,038 control chromosomes in the GnomAD database, including 9,476 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 0.33 (9473 hom., cov: 32)
  • Exomes 𝑓: 0.37 (3 hom.)
• Consequence: MARK2P9 NR_038243.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.83

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=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MARK2P9	NR_038243.2	n.611C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MARK2P9	ENST00000430958.1	n.605C>T		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50466 AN: 151890 Hom.: 9476 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.343

GnomAD4 exome AF: 0.367 AC: 11 AN: 30 Hom.: 3 Cov.: 0 AF XY: 0.292 AC XY: 7 AN XY: 24

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 NFE exome AF: 0.318

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.332 AC: 50484 AN: 152008 Hom.: 9473 Cov.: 32 AF XY: 0.341 AC XY: 25328 AN XY: 74320

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.342

Alfa AF: 0.324 Hom.: 7730

Bravo AF: 0.336

Asia WGS AF: 0.586 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	0.42
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2209972; hg19: chr10-94179028;