chr6-9770858-C-T

Position:

• chr6-9770858-C-T

Variant summary

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

The NR_170155.1(OFCC1):​n.1289-1803G>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 0.266 in 152,004 control chromosomes in the GnomAD database, including 5,637 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 0.27 (5637 hom., cov: 33)
• Consequence: OFCC1 NR_170155.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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 (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OFCC1	NR_170155.1	n.1289-1803G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000492094.6	n.1572-1803G>A		intron_variant, non_coding_transcript_variant		5
OFCC1	ENST00000642964.1	n.1593-1803G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40453 AN: 151886 Hom.: 5627 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0514

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.266 AC: 40508 AN: 152004 Hom.: 5637 Cov.: 33 AF XY: 0.271 AC XY: 20120 AN XY: 74302

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.0519

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.269

Alfa AF: 0.270 Hom.: 3091

Bravo AF: 0.251

Asia WGS AF: 0.208 AC: 721 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.79
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1328132; hg19: chr6-9771091;