10-27288686-T-G

Variant names:

• chr10-27288686-T-G
• rs11015640
• ENST00000438905.2:n.569T>G

Variant summary

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

The ENST00000438905.2(ODAD2P1):​n.569T>G 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 0.413 in 1,439,646 control chromosomes in the GnomAD database, including 124,165 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 0.41 (13008 hom., cov: 31)
  • Exomes 𝑓: 0.41 (111157 hom.)
• Consequence: ODAD2P1 ENST00000438905.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODAD2P1	NR_138082.1	n.505T>G		non_coding_transcript_exon_variant	Exon 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODAD2P1	ENST00000438905.2	n.569T>G		non_coding_transcript_exon_variant	Exon 4 of 4	6
ENSG00000262412	ENST00000576034.6	n.510T>G		non_coding_transcript_exon_variant	Exon 4 of 5	2
ENSG00000262412	ENST00000787620.1	n.163T>G		non_coding_transcript_exon_variant	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62243 AN: 151768 Hom.: 13018 Cov.: 31

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.430

GnomAD4 exome AF: 0.413 AC: 532432 AN: 1287760 Hom.: 111157 Cov.: 19 AF XY: 0.418 AC XY: 269378 AN XY: 643846

African (AFR) AF: 0.323 AC: 9497 AN: 29390

American (AMR) AF: 0.354 AC: 13301 AN: 37534

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 9644 AN: 22704

East Asian (EAS) AF: 0.339 AC: 13130 AN: 38778

South Asian (SAS) AF: 0.498 AC: 37527 AN: 75346

European-Finnish (FIN) AF: 0.414 AC: 21370 AN: 51602

Middle Eastern (MID) AF: 0.533 AC: 2818 AN: 5284

European-Non Finnish (NFE) AF: 0.413 AC: 402242 AN: 973028

Other (OTH) AF: 0.423 AC: 22903 AN: 54094

GnomAD4 genome AF: 0.410 AC: 62235 AN: 151886 Hom.: 13008 Cov.: 31 AF XY: 0.411 AC XY: 30506 AN XY: 74246

African (AFR) AF: 0.337 AC: 13956 AN: 41420

American (AMR) AF: 0.378 AC: 5758 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1515 AN: 3468

East Asian (EAS) AF: 0.386 AC: 1995 AN: 5164

South Asian (SAS) AF: 0.504 AC: 2426 AN: 4816

European-Finnish (FIN) AF: 0.431 AC: 4534 AN: 10520

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

European-Non Finnish (NFE) AF: 0.449 AC: 30536 AN: 67938

Other (OTH) AF: 0.426 AC: 897 AN: 2108

Alfa AF: 0.271 Hom.: 659

Bravo AF: 0.403

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.65
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs11015640; hg19: chr10-27577615;