rs4712416

chr6-10180332-G-Achr6-10180332-G-Cchr6-10180332-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.232-20833C>T 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 0.165 in 152,040 control chromosomes in the GnomAD database, including 2,352 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 0.17 (2352 hom., cov: 33)
• Consequence: OFCC1 NR_170155.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OFCC1	NR_170155.1	n.232-20833C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000462111.1	n.164-20833C>T		intron_variant, non_coding_transcript_variant		1
	ENST00000481704.1	n.232-20833C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25097 AN: 151922 Hom.: 2355 Cov.: 33

Gnomad AFR AF: 0.0955

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.0577

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.165 AC: 25100 AN: 152040 Hom.: 2352 Cov.: 33 AF XY: 0.168 AC XY: 12458 AN XY: 74304

Gnomad4 AFR AF: 0.0953

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.166

Alfa AF: 0.170 Hom.: 3491

Bravo AF: 0.160

Asia WGS AF: 0.311 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.0
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4712416; hg19: chr6-10180565;