rs6906469

Variant names:

• chr6-10018401-G-C
• rs6906469
• ENST00000481704.1:n.338-79052C>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000481704.1(OFCC1):​n.338-79052C>G variant causes a intron change. The variant allele was found at a frequency of 0.153 in 152,222 control chromosomes in the GnomAD database, including 2,321 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 0.15 (2321 hom., cov: 33)
• Consequence: OFCC1 ENST00000481704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.14

Genes affected

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

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OFCC1	NR_170155.1	n.338-79052C>G		intron_variant	Intron 2 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OFCC1	ENST00000481704.1	n.338-79052C>G		intron_variant	Intron 2 of 2	1
OFCC1	ENST00000485268.1	n.162+42249C>G		intron_variant	Intron 2 of 4	1
OFCC1	ENST00000472329.5	n.116+42249C>G		intron_variant	Intron 1 of 7	2

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23236 AN: 152104 Hom.: 2316 Cov.: 33

Gnomad AFR AF: 0.0402

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0694

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.153 AC: 23243 AN: 152222 Hom.: 2321 Cov.: 33 AF XY: 0.159 AC XY: 11835 AN XY: 74408

Gnomad4 AFR AF: 0.0402

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.0694

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.163

Alfa AF: 0.174 Hom.: 347

Bravo AF: 0.141

Asia WGS AF: 0.110 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	19
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6906469; hg19: chr6-10018634;