rs67373796

chr6-9990418-T-G

Variant summary

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

The NR_170155.1(OFCC1):n.338-51069A>C 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 0.121 in 152,184 control chromosomes in the GnomAD database, including 1,656 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 0.12 (1656 hom., cov: 32)
• Consequence: OFCC1 NR_170155.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OFCC1	NR_170155.1	n.338-51069A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000481704.1	n.338-51069A>C		intron_variant, non_coding_transcript_variant		1
	ENST00000485268.1	n.163-42956A>C		intron_variant, non_coding_transcript_variant		1
	ENST00000472329.5	n.117-51069A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18343 AN: 152066 Hom.: 1651 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0694

Gnomad ASJ AF: 0.0551

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0401

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.0951

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

GnomAD4 genome AF: 0.121 AC: 18370 AN: 152184 Hom.: 1656 Cov.: 32 AF XY: 0.118 AC XY: 8784 AN XY: 74420

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.0691

Gnomad4 ASJ AF: 0.0551

Gnomad4 EAS AF: 0.0849

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0401

Gnomad4 NFE AF: 0.0700

Gnomad4 OTH AF: 0.0989

Alfa AF: 0.101 Hom.: 166

Bravo AF: 0.128

Asia WGS AF: 0.140 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.6
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs67373796; hg19: chr6-9990651;