rs67373796

Variant names:

• chr6-9990418-T-G
• rs67373796
• ENST00000481704.1:n.338-51069A>C

Variant summary

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

The ENST00000481704.1(ENSG00000293385):​n.338-51069A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,184 control chromosomes in the GnomAD database, including 1,656 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 0.12 (1656 hom., cov: 32)
• Consequence: ENSG00000293385 ENST00000481704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OFCC1	NR_170155.1	n.338-51069A>C		intron_variant	Intron 2 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293385	ENST00000481704.1	n.338-51069A>C		intron_variant	Intron 2 of 2	1
ENSG00000293385	ENST00000485268.1	n.163-42956A>C		intron_variant	Intron 2 of 4	1
ENSG00000293385	ENST00000472329.5	n.117-51069A>C		intron_variant	Intron 1 of 7	2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18343 AN: 152066 Hom.: 1651 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0694

Gnomad ASJ AF: 0.0551

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0401

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.0951

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

GnomAD4 genome AF: 0.121 AC: 18370 AN: 152184 Hom.: 1656 Cov.: 32 AF XY: 0.118 AC XY: 8784 AN XY: 74420

African (AFR) AF: 0.255 AC: 10572 AN: 41484

American (AMR) AF: 0.0691 AC: 1057 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0551 AC: 191 AN: 3468

East Asian (EAS) AF: 0.0849 AC: 440 AN: 5180

South Asian (SAS) AF: 0.133 AC: 641 AN: 4830

European-Finnish (FIN) AF: 0.0401 AC: 426 AN: 10614

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0700 AC: 4760 AN: 68002

Other (OTH) AF: 0.0989 AC: 209 AN: 2114

Alfa AF: 0.101 Hom.: 166

Bravo AF: 0.128

Asia WGS AF: 0.140 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.52
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs67373796; hg19: chr6-9990651;