rs4712416

Variant names:

• chr6-10180332-G-A
• rs4712416
• ENST00000462111.1:n.164-20833C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-10180332-G-A
• chr6-10180332-G-C
• chr6-10180332-G-T

Variant summary

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

The ENST00000462111.1(ENSG00000293385):​n.164-20833C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,040 control chromosomes in the GnomAD database, including 2,352 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 0.17 (2352 hom., cov: 33)
• Consequence: ENSG00000293385 ENST00000462111.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000462111.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OFCC1	NR_170155.1		n.232-20833C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293385	ENST00000462111.1	TSL:1	n.164-20833C>T		intron	N/A
	ENSG00000293385	ENST00000481704.1	TSL:1	n.232-20833C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25097 AN: 151922 Hom.: 2355 Cov.: 33

Gnomad AFR AF: 0.0955

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.0577

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.165 AC: 25100 AN: 152040 Hom.: 2352 Cov.: 33 AF XY: 0.168 AC XY: 12458 AN XY: 74304

African (AFR) AF: 0.0953 AC: 3959 AN: 41530

American (AMR) AF: 0.144 AC: 2200 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3472

East Asian (EAS) AF: 0.413 AC: 2133 AN: 5168

South Asian (SAS) AF: 0.240 AC: 1149 AN: 4790

European-Finnish (FIN) AF: 0.202 AC: 2135 AN: 10582

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.187 AC: 12666 AN: 67904

Other (OTH) AF: 0.166 AC: 348 AN: 2102

Alfa AF: 0.174 Hom.: 8419

Bravo AF: 0.160

Asia WGS AF: 0.311 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.77
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs4712416; hg19: chr6-10180565;