10-92419591-G-T

Variant names:

• chr10-92419591-G-T
• rs967878
• ENST00000430958.1:n.925G>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.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
• Publications: 4 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=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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.931G>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.925G>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000304764	ENST00000806156.1		n.874C>A		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.600 AC: 6 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.337 AC: 31 AN: 92

Other (OTH) AF: 0.700 AC: 7 AN: 10

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

African (AFR) AF: 0.711 AC: 29478 AN: 41464

American (AMR) AF: 0.529 AC: 8077 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1462 AN: 3472

East Asian (EAS) AF: 0.836 AC: 4320 AN: 5168

South Asian (SAS) AF: 0.721 AC: 3465 AN: 4804

European-Finnish (FIN) AF: 0.448 AC: 4738 AN: 10580

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29598 AN: 67952

Other (OTH) AF: 0.506 AC: 1066 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.77
DANN	Benign	0.27
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs967878; hg19: chr10-94179348;