rs3756814

Positions:

• chr6-24705607-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_030939.5(C6orf62):​c.*530A>G variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.328 in 152,612 control chromosomes in the GnomAD database, including 8,625 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 0.33 (8593 hom., cov: 33)
  • Exomes 𝑓: 0.38 (32 hom.)
• Consequence: C6orf62 NM_030939.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.07

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C6orf62	NM_030939.5	c.*530A>G		3_prime_UTR_variant	5/5	ENST00000378119.9	NP_112201.1
C6orf62	NM_001410835.1	c.*530A>G		3_prime_UTR_variant	5/5		NP_001397764.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C6orf62	ENST00000378119.9	c.*530A>G		3_prime_UTR_variant	5/5	1	NM_030939.5	ENSP00000367359	P1
C6orf62	ENST00000710317.1	c.*530A>G		3_prime_UTR_variant	5/5			ENSP00000518198	P1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49837 AN: 152066 Hom.: 8595 Cov.: 33

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.316

GnomAD4 exome AF: 0.376 AC: 161 AN: 428 Hom.: 32 Cov.: 0 AF XY: 0.366 AC XY: 96 AN XY: 262

Gnomad4 FIN exome AF: 0.371

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.328 AC: 49847 AN: 152184 Hom.: 8593 Cov.: 33 AF XY: 0.324 AC XY: 24137 AN XY: 74400

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.314

Alfa AF: 0.369 Hom.: 5765

Bravo AF: 0.319

Asia WGS AF: 0.287 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	19
DANN	Benign	0.92

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: rs3756814; hg19: chr6-24705835;