rs4716055

Variant names:

• chr6-9853686-G-T
• rs4716055
• ENST00000460363.6:n.363-43972C>A

Variant summary

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

The ENST00000460363.6(ENSG00000293385):​n.363-43972C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 152,112 control chromosomes in the GnomAD database, including 63,707 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 0.91 (63707 hom., cov: 31)
• Consequence: ENSG00000293385 ENST00000460363.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 13 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OFCC1	NR_170155.1	n.730-8093C>A		intron_variant	Intron 6 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293385	ENST00000460363.6	n.363-43972C>A		intron_variant	Intron 4 of 7	1
ENSG00000293385	ENST00000469426.5	n.671-3217C>A		intron_variant	Intron 6 of 11	1
ENSG00000293385	ENST00000486246.5	n.511-3217C>A		intron_variant	Intron 5 of 8	1

Frequencies

GnomAD3 genomes AF: 0.914 AC: 138952 AN: 151994 Hom.: 63664 Cov.: 31

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.914 AC: 139052 AN: 152112 Hom.: 63707 Cov.: 31 AF XY: 0.917 AC XY: 68207 AN XY: 74366

African (AFR) AF: 0.964 AC: 40019 AN: 41524

American (AMR) AF: 0.938 AC: 14330 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3191 AN: 3472

East Asian (EAS) AF: 0.992 AC: 5123 AN: 5162

South Asian (SAS) AF: 0.967 AC: 4657 AN: 4818

European-Finnish (FIN) AF: 0.892 AC: 9440 AN: 10578

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59194 AN: 67960

Other (OTH) AF: 0.922 AC: 1948 AN: 2112

Alfa AF: 0.893 Hom.: 117922

Bravo AF: 0.922

Asia WGS AF: 0.946 AC: 3287 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.43
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4716055; hg19: chr6-9853919;