rs13195786

Variant names:

• chr6-10163735-A-G
• rs13195786
• ENST00000462111.1:n.164-4236T>C

Variant summary

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

The ENST00000462111.1(ENSG00000293385):​n.164-4236T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0988 in 152,282 control chromosomes in the GnomAD database, including 912 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 0.099 (912 hom., cov: 33)
• Consequence: ENSG00000293385 ENST00000462111.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 12 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=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OFCC1	NR_170155.1	n.232-4236T>C		intron_variant	Intron 1 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293385	ENST00000462111.1	n.164-4236T>C		intron_variant	Intron 1 of 2	1
ENSG00000293385	ENST00000481704.1	n.232-4236T>C		intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes AF: 0.0989 AC: 15045 AN: 152164 Hom.: 913 Cov.: 33

Gnomad AFR AF: 0.0318

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0917

Gnomad ASJ AF: 0.0547

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0988 AC: 15051 AN: 152282 Hom.: 912 Cov.: 33 AF XY: 0.0994 AC XY: 7403 AN XY: 74452

African (AFR) AF: 0.0317 AC: 1317 AN: 41562

American (AMR) AF: 0.0916 AC: 1402 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0547 AC: 190 AN: 3472

East Asian (EAS) AF: 0.186 AC: 966 AN: 5182

South Asian (SAS) AF: 0.112 AC: 540 AN: 4828

European-Finnish (FIN) AF: 0.126 AC: 1340 AN: 10596

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 9013 AN: 68024

Other (OTH) AF: 0.103 AC: 217 AN: 2112

Alfa AF: 0.123 Hom.: 2777

Bravo AF: 0.0945

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	5.5
DANN	Benign	0.74
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs13195786; hg19: chr6-10163968;