rs4716055

chr6-9853686-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_170155.1(OFCC1):n.730-8093C>A variant causes a intron, non coding transcript 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: OFCC1 NR_170155.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

Genes affected

(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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
OFCC1	NR_170155.1	n.730-8093C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000492094.6	n.536-8093C>A		intron_variant, non_coding_transcript_variant		5
OFCC1	ENST00000642964.1	n.557-8093C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.964

Gnomad4 AMR AF: 0.938

Gnomad4 ASJ AF: 0.919

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.967

Gnomad4 FIN AF: 0.892

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.922

Alfa AF: 0.884 Hom.: 61055

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4716055; hg19: chr6-9853919;