chr6-24721069-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001410835.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C6orf62	NM_001410835.1		c.-1168G>A		upstream_gene	N/A	NP_001397764.1	Q9GZU0-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C6orf62	ENST00000710317.1		c.-2401G>A		upstream_gene	N/A	ENSP00000518198.1	Q9GZU0-1
	C6orf62	ENST00000853646.1		c.-1235G>A		upstream_gene	N/A	ENSP00000523705.1
	C6orf62	ENST00000853647.1		c.-1415G>A		upstream_gene	N/A	ENSP00000523706.1

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

African (AFR) AF: 0.321 AC: 13326 AN: 41454

American (AMR) AF: 0.183 AC: 2799 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 754 AN: 3470

East Asian (EAS) AF: 0.0129 AC: 67 AN: 5184

South Asian (SAS) AF: 0.127 AC: 615 AN: 4826

European-Finnish (FIN) AF: 0.250 AC: 2648 AN: 10580

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16168 AN: 67970

Other (OTH) AF: 0.233 AC: 491 AN: 2110

Alfa AF: 0.236 Hom.: 1969

Bravo AF: 0.245

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.060
DANN	Benign	0.57
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6456632; hg19: chr6-24721297;