rs1328132

Variant names:

• chr6-9770858-C-T
• rs1328132
• ENST00000460363.6:n.584-1803G>A

Variant summary

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

The ENST00000460363.6(ENSG00000293385):​n.584-1803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,004 control chromosomes in the GnomAD database, including 5,637 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 0.27 (5637 hom., cov: 33)
• Consequence: ENSG00000293385 ENST00000460363.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 2 publications found

Genes affected

ENSG00000293385 (HGNC:):

OFCC1 (HGNC:21017): (orofacial cleft 1 candidate 1) Predicted to be located in cytosol; endoplasmic reticulum; and microtubule cytoskeleton. Predicted to be active in perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OFCC1	NR_170155.1	n.1289-1803G>A		intron_variant	Intron 10 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293385	ENST00000460363.6	n.584-1803G>A		intron_variant	Intron 6 of 7	1
ENSG00000293385	ENST00000487015.5	n.864-1803G>A		intron_variant	Intron 7 of 9	1
ENSG00000293385	ENST00000492169.5	n.395-1803G>A		intron_variant	Intron 5 of 6	1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40453 AN: 151886 Hom.: 5627 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0514

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.266 AC: 40508 AN: 152004 Hom.: 5637 Cov.: 33 AF XY: 0.271 AC XY: 20120 AN XY: 74302

African (AFR) AF: 0.255 AC: 10572 AN: 41450

American (AMR) AF: 0.246 AC: 3763 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 689 AN: 3472

East Asian (EAS) AF: 0.0519 AC: 269 AN: 5184

South Asian (SAS) AF: 0.276 AC: 1331 AN: 4820

European-Finnish (FIN) AF: 0.390 AC: 4114 AN: 10542

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18917 AN: 67952

Other (OTH) AF: 0.269 AC: 568 AN: 2110

Alfa AF: 0.271 Hom.: 3411

Bravo AF: 0.251

Asia WGS AF: 0.208 AC: 721 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.79
DANN	Benign	0.47
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1328132; hg19: chr6-9771091;