6-10175803-G-A

Variant names:

• chr6-10175803-G-A
• rs12210761
• ENST00000462111.1:n.164-16304C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000462111.1(ENSG00000293385):​n.164-16304C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0374 in 152,224 control chromosomes in the GnomAD database, including 103 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 0.037 (103 hom., cov: 33)
• Consequence: ENSG00000293385 ENST00000462111.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.989
• Publications: 6 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=-0.68).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0374 (5692/152224) while in subpopulation SAS AF = 0.0449 (217/4828). AF 95% confidence interval is 0.0417. There are 103 homozygotes in GnomAd4. There are 2722 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 103 gene

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OFCC1	NR_170155.1		n.232-16304C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293385	ENST00000462111.1	TSL:1	n.164-16304C>T		intron	N/A
	ENSG00000293385	ENST00000481704.1	TSL:1	n.232-16304C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0373 AC: 5681 AN: 152106 Hom.: 101 Cov.: 33

Gnomad AFR AF: 0.0363

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0216

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.0443

Gnomad FIN AF: 0.0300

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0429

Gnomad OTH AF: 0.0288

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

GnomAD4 genome AF: 0.0374 AC: 5692 AN: 152224 Hom.: 103 Cov.: 33 AF XY: 0.0366 AC XY: 2722 AN XY: 74440

African (AFR) AF: 0.0362 AC: 1505 AN: 41528

American (AMR) AF: 0.0216 AC: 330 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3466

East Asian (EAS) AF: 0.0375 AC: 194 AN: 5178

South Asian (SAS) AF: 0.0449 AC: 217 AN: 4828

European-Finnish (FIN) AF: 0.0300 AC: 318 AN: 10602

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0429 AC: 2921 AN: 68010

Other (OTH) AF: 0.0294 AC: 62 AN: 2108

Alfa AF: 0.0398 Hom.: 360

Bravo AF: 0.0356

Asia WGS AF: 0.0430 AC: 150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	10
DANN	Benign	0.72
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs12210761; hg19: chr6-10176036;