rs116201121

chr6-9993504-G-Achr6-9993504-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NR_170155.1(OFCC1):n.338-54155C>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 0.00648 in 152,202 control chromosomes in the GnomAD database, including 5 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 0.0065 (5 hom., cov: 31)
• Consequence: OFCC1 NR_170155.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS2: High Homozygotes in GnomAd at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OFCC1	NR_170155.1	n.338-54155C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000481704.1	n.338-54155C>T		intron_variant, non_coding_transcript_variant		1
	ENST00000485268.1	n.163-46042C>T		intron_variant, non_coding_transcript_variant		1
	ENST00000472329.5	n.117-54155C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.00649 AC: 987 AN: 152084 Hom.: 5 Cov.: 31

Gnomad AFR AF: 0.00208

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000918

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00518

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.00336

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

GnomAD4 genome AF: 0.00648 AC: 987 AN: 152202 Hom.: 5 Cov.: 31 AF XY: 0.00654 AC XY: 487 AN XY: 74412

Gnomad4 AFR AF: 0.00207

Gnomad4 AMR AF: 0.000917

Gnomad4 ASJ AF: 0.00893

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00518

Gnomad4 FIN AF: 0.0123

Gnomad4 NFE AF: 0.0102

Gnomad4 OTH AF: 0.00333

Alfa AF: 0.00379 Hom.: 2

Bravo AF: 0.00525

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.16
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs116201121; hg19: chr6-9993737;