1-186432074-G-T

Variant names:

• chr1-186432074-G-T
• rs7556360
• XM_047423438.1:c.*6953G>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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660380.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDC-AS1	ENST00000660380.1		n.1740-3151G>T		intron	N/A
	PDC-AS1	ENST00000665030.1		n.1961+725G>T		intron	N/A

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 v4.9

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;