rs2209972

Variant names:

• chr10-92419271-C-T
• rs2209972
• ENST00000430958.1:n.605C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

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

ENSG00000304764 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_038243.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MARK2P9	NR_038243.2		n.611C>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MARK2P9	ENST00000430958.1	TSL:6	n.605C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000304764	ENST00000806156.1		n.1194G>A		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.318 AC: 7 AN: 22

Other (OTH) AF: 0.500 AC: 2 AN: 4

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

African (AFR) AF: 0.232 AC: 9630 AN: 41440

American (AMR) AF: 0.414 AC: 6320 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1236 AN: 3470

East Asian (EAS) AF: 0.765 AC: 3943 AN: 5156

South Asian (SAS) AF: 0.553 AC: 2663 AN: 4812

European-Finnish (FIN) AF: 0.338 AC: 3574 AN: 10582

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21708 AN: 67972

Other (OTH) AF: 0.342 AC: 720 AN: 2108

Alfa AF: 0.323 Hom.: 10115

Bravo AF: 0.336

Asia WGS AF: 0.586 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	0.42
DANN	Benign	0.64
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs2209972; hg19: chr10-94179028;