chr6-10175803-G-A

Position:

• chr6-10175803-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_170155.1(OFCC1):​n.232-16304C>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 0.0374 in 152,224 control chromosomes in the GnomAD database, including 103 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 0.037 (103 hom., cov: 33)
• Consequence: OFCC1 NR_170155.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.989

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0374 (5692/152224) while in subpopulation SAS AF= 0.0449 (217/4828). AF 95% confidence interval is 0.0417. There are 103 homozygotes in gnomad4. There are 2722 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 103 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OFCC1	NR_170155.1	n.232-16304C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000462111.1	n.164-16304C>T		intron_variant, non_coding_transcript_variant		1
	ENST00000481704.1	n.232-16304C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0373 AC: 5681 AN: 152106 Hom.: 101 Cov.: 33

Gnomad AFR AF: 0.0363

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0216

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.0443

Gnomad FIN AF: 0.0300

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0429

Gnomad OTH AF: 0.0288

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

GnomAD4 genome AF: 0.0374 AC: 5692 AN: 152224 Hom.: 103 Cov.: 33 AF XY: 0.0366 AC XY: 2722 AN XY: 74440

Gnomad4 AFR AF: 0.0362

Gnomad4 AMR AF: 0.0216

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.0375

Gnomad4 SAS AF: 0.0449

Gnomad4 FIN AF: 0.0300

Gnomad4 NFE AF: 0.0429

Gnomad4 OTH AF: 0.0294

Alfa AF: 0.0379 Hom.: 168

Bravo AF: 0.0356

Asia WGS AF: 0.0430 AC: 150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	10
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12210761; hg19: chr6-10176036;