rs17378130

Positions:

• chr8-123229102-C-T

Variant summary

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

The NM_032847.3(C8orf76):​c.815+2198G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0846 in 151,878 control chromosomes in the GnomAD database, including 735 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 0.085 (735 hom., cov: 32)
• Consequence: C8orf76 NM_032847.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

Genes affected

C8orf76 (HGNC:25924): (chromosome 8 open reading frame 76)

ZHX1-C8orf76 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C8orf76	NM_032847.3	c.815+2198G>A		intron_variant		ENST00000276704.6
ZHX1-C8orf76	NM_001204180.2	c.719+2198G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C8orf76	ENST00000276704.6	c.815+2198G>A		intron_variant		1	NM_032847.3	P1
C8orf76	ENST00000517760.1	n.293+2198G>A		intron_variant, non_coding_transcript_variant		2
C8orf76	ENST00000519791.5	n.334-2470G>A		intron_variant, non_coding_transcript_variant		2
C8orf76	ENST00000521310.5	n.813+2198G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0847 AC: 12849 AN: 151760 Hom.: 735 Cov.: 32

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0540

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.0957

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

GnomAD4 genome AF: 0.0846 AC: 12846 AN: 151878 Hom.: 735 Cov.: 32 AF XY: 0.0829 AC XY: 6155 AN XY: 74276

Gnomad4 AFR AF: 0.0224

Gnomad4 AMR AF: 0.0690

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0545

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.0946

Alfa AF: 0.117 Hom.: 1254

Bravo AF: 0.0796

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.2
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17378130; hg19: chr8-124241342;