6-10180655-C-T

Variant names:

• chr6-10180655-C-T
• rs4712419
• ENST00000462111.1:n.164-21156G>A

Variant summary

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

The ENST00000462111.1(ENSG00000293385):​n.164-21156G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,148 control chromosomes in the GnomAD database, including 2,208 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 (2208 hom., cov: 32)
• Consequence: ENSG00000293385 ENST00000462111.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 0 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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 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.232-21156G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293385	ENST00000462111.1	TSL:1	n.164-21156G>A		intron	N/A
	ENSG00000293385	ENST00000481704.1	TSL:1	n.232-21156G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23435 AN: 152028 Hom.: 2211 Cov.: 32

Gnomad AFR AF: 0.0584

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.0545

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.154 AC: 23434 AN: 152148 Hom.: 2208 Cov.: 32 AF XY: 0.158 AC XY: 11724 AN XY: 74366

African (AFR) AF: 0.0582 AC: 2416 AN: 41542

American (AMR) AF: 0.140 AC: 2142 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2104 AN: 5150

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4826

European-Finnish (FIN) AF: 0.202 AC: 2136 AN: 10568

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.186 AC: 12654 AN: 67968

Other (OTH) AF: 0.152 AC: 322 AN: 2116

Alfa AF: 0.164 Hom.: 289

Bravo AF: 0.147

Asia WGS AF: 0.309 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	4.6
DANN	Benign	0.84
PhyloP100		0.086

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4712419;

hg19: chr6-10180888;