rs3813687

chr6-24719750-G-Achr6-24719750-G-T

Variant summary

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

The ENST00000710317.1(C6orf62):c.-1082C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,539,796 control chromosomes in the GnomAD database, including 24,754 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 0.13 (1632 hom., cov: 31)
  • Exomes 𝑓: 0.18 (23122 hom.)
• Consequence: C6orf62 ENST00000710317.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C6orf62	NM_001410835.1	c.42+110C>T		intron_variant
C6orf62	XM_047419384.1	c.42+110C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C6orf62	ENST00000710317.1	c.-1082C>T		5_prime_UTR_variant	1/5			P1
C6orf62	ENST00000378102.3	c.42+110C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19930 AN: 151924 Hom.: 1633 Cov.: 31

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.100

GnomAD4 exome AF: 0.178 AC: 246753 AN: 1387752 Hom.: 23122 Cov.: 41 AF XY: 0.175 AC XY: 119798 AN XY: 684134

Gnomad4 AFR exome AF: 0.0266

Gnomad4 AMR exome AF: 0.147

Gnomad4 ASJ exome AF: 0.162

Gnomad4 EAS exome AF: 0.121

Gnomad4 SAS exome AF: 0.106

Gnomad4 FIN exome AF: 0.195

Gnomad4 NFE exome AF: 0.191

Gnomad4 OTH exome AF: 0.158

GnomAD4 genome AF: 0.131 AC: 19927 AN: 152044 Hom.: 1632 Cov.: 31 AF XY: 0.131 AC XY: 9721 AN XY: 74312

Gnomad4 AFR AF: 0.0320

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.0979

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.0992

Alfa AF: 0.167 Hom.: 2559

Bravo AF: 0.125

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	16
Dann	Benign	0.83
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs3813687; hg19: chr6-24719978;