chr10-27271191-C-T

Variant names:

• chr10-27271191-C-T
• rs10829219
• ENST00000438905.2:n.259-7879C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000576034.6(ENSG00000262412):​n.404+7977C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,936 control chromosomes in the GnomAD database, including 14,520 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 0.42 (14520 hom., cov: 32)
• Consequence: ENSG00000262412 ENST00000576034.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 11 publications found

Genes affected

ODAD2P1 (HGNC:44937): (outer dynein arm docking complex subunit 2 pseudogene 1)

ENSG00000262412 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000576034.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODAD2P1	NR_138082.1		n.399+7977C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODAD2P1	ENST00000438905.2	TSL:6	n.259-7879C>T		intron	N/A
	ENSG00000262412	ENST00000576034.6	TSL:2	n.404+7977C>T		intron	N/A
	ENSG00000262412	ENST00000787620.1		n.154-17486C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63222 AN: 151816 Hom.: 14533 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.416 AC: 63203 AN: 151936 Hom.: 14520 Cov.: 32 AF XY: 0.420 AC XY: 31198 AN XY: 74272

African (AFR) AF: 0.199 AC: 8234 AN: 41424

American (AMR) AF: 0.463 AC: 7068 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1731 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2104 AN: 5156

South Asian (SAS) AF: 0.463 AC: 2226 AN: 4806

European-Finnish (FIN) AF: 0.523 AC: 5500 AN: 10526

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34734 AN: 67970

Other (OTH) AF: 0.437 AC: 921 AN: 2106

Alfa AF: 0.484 Hom.: 80356

Bravo AF: 0.405

Asia WGS AF: 0.409 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.5
DANN	Benign	0.31
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs10829219; hg19: chr10-27560120;