6-24721069-C-T

Variant names:

• chr6-24721069-C-T
• rs6456632
• ENST00000710317.1:c.-2401G>A

Variant summary

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

The NM_001410835.1(C6orf62):​c.-1168G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,086 control chromosomes in the GnomAD database, including 4,826 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 0.24 (4826 hom., cov: 33)
• Consequence: C6orf62 NM_001410835.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

Genes affected

C6orf62 (HGNC:20998): (chromosome 6 open reading frame 62)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C6orf62	NM_001410835.1	c.-1168G>A		upstream_gene_variant			NP_001397764.1
C6orf62	XM_047419384.1	c.-1168G>A		upstream_gene_variant			XP_047275340.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C6orf62	ENST00000710317.1	c.-2401G>A		upstream_gene_variant				ENSP00000518198.1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37156 AN: 151968 Hom.: 4817 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.245 AC: 37197 AN: 152086 Hom.: 4826 Cov.: 33 AF XY: 0.242 AC XY: 17983 AN XY: 74370

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.0129

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.233

Alfa AF: 0.240 Hom.: 1145

Bravo AF: 0.245

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.060
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6456632; hg19: chr6-24721297;