1-186432074-G-T

Variant names:

• chr1-186432074-G-T
• rs7556360
• XR_007061319.1:n.2566G>T

Variant summary

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

The XR_007061319.1(ODR4):​n.2566G>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 0.333 in 151,974 control chromosomes in the GnomAD database, including 9,271 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 (9271 hom., cov: 31)
• Consequence: ODR4 XR_007061319.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• Publications: 1 publications found

Genes affected

ODR4 (HGNC:24299): (odr-4 GPCR localization factor homolog) Predicted to be involved in protein localization. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

PDC-AS1 (HGNC:40432): (PDC antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODR4	XR_007061319.1	n.2566G>T		non_coding_transcript_exon_variant	Exon 16 of 16
ODR4	XM_047423438.1	c.*6953G>T		3_prime_UTR_variant	Exon 15 of 15		XP_047279394.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDC-AS1	ENST00000660380.1	n.1740-3151G>T		intron_variant	Intron 1 of 5
PDC-AS1	ENST00000665030.1	n.1961+725G>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50484 AN: 151856 Hom.: 9227 Cov.: 31

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.333 AC: 50573 AN: 151974 Hom.: 9271 Cov.: 31 AF XY: 0.332 AC XY: 24698 AN XY: 74308

African (AFR) AF: 0.480 AC: 19868 AN: 41424

American (AMR) AF: 0.373 AC: 5684 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1096 AN: 3468

East Asian (EAS) AF: 0.423 AC: 2184 AN: 5160

South Asian (SAS) AF: 0.255 AC: 1232 AN: 4824

European-Finnish (FIN) AF: 0.218 AC: 2300 AN: 10566

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17177 AN: 67964

Other (OTH) AF: 0.346 AC: 729 AN: 2104

Alfa AF: 0.291 Hom.: 918

Bravo AF: 0.357

Asia WGS AF: 0.395 AC: 1372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.46
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7556360; hg19: chr1-186401206;