rs3756814

Variant names:

• chr6-24705607-T-C
• rs3756814
• NM_030939.5:c.*530A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030939.5. 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_030939.5	MANE Select	c.*530A>G		3_prime_UTR	Exon 5 of 5	NP_112201.1
	C6orf62	NM_001410835.1		c.*530A>G		3_prime_UTR	Exon 5 of 5	NP_001397764.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C6orf62	ENST00000378119.9	TSL:1 MANE Select	c.*530A>G		3_prime_UTR	Exon 5 of 5	ENSP00000367359.4
	C6orf62	ENST00000853648.1		c.*530A>G		3_prime_UTR	Exon 6 of 6	ENSP00000523707.1
	C6orf62	ENST00000710317.1		c.*530A>G		3_prime_UTR	Exon 5 of 5	ENSP00000518198.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.371 AC: 156 AN: 420

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 3 AN: 4

Other (OTH) AF: 0.500 AC: 2 AN: 4

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

African (AFR) AF: 0.230 AC: 9570 AN: 41552

American (AMR) AF: 0.304 AC: 4646 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1343 AN: 3468

East Asian (EAS) AF: 0.207 AC: 1075 AN: 5184

South Asian (SAS) AF: 0.386 AC: 1863 AN: 4824

European-Finnish (FIN) AF: 0.361 AC: 3815 AN: 10578

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26315 AN: 67984

Other (OTH) AF: 0.314 AC: 663 AN: 2112

Alfa AF: 0.363 Hom.: 9253

Bravo AF: 0.319

Asia WGS AF: 0.287 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	19
DANN	Benign	0.92
PhyloP100		4.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3756814; hg19: chr6-24705835;