rs2294686

Variant names:

• chr6-24708974-A-G
• rs2294686
• NM_030939.5:c.430-63T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030939.5(C6orf62):​c.430-63T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0584 in 1,604,772 control chromosomes in the GnomAD database, including 10,980 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 0.10 (1886 hom., cov: 32)
  • Exomes 𝑓: 0.054 (9094 hom.)
• Consequence: C6orf62 NM_030939.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 3 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C6orf62	NM_030939.5	c.430-63T>C		intron_variant	Intron 3 of 4	ENST00000378119.9	NP_112201.1
C6orf62	NM_001410835.1	c.343-63T>C		intron_variant	Intron 3 of 4		NP_001397764.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C6orf62	ENST00000378119.9	c.430-63T>C		intron_variant	Intron 3 of 4	1	NM_030939.5	ENSP00000367359.4
C6orf62	ENST00000710317.1	c.430-63T>C		intron_variant	Intron 3 of 4			ENSP00000518198.1
C6orf62	ENST00000378102.3	c.343-63T>C		intron_variant	Intron 3 of 4	5		ENSP00000367342.3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15886 AN: 152156 Hom.: 1878 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0108

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0182

Gnomad OTH AF: 0.102

GnomAD4 exome AF: 0.0535 AC: 77773 AN: 1452498 Hom.: 9094 Cov.: 31 AF XY: 0.0533 AC XY: 38451 AN XY: 721552

African (AFR) AF: 0.183 AC: 6076 AN: 33148

American (AMR) AF: 0.349 AC: 15265 AN: 43698

Ashkenazi Jewish (ASJ) AF: 0.0269 AC: 697 AN: 25906

East Asian (EAS) AF: 0.463 AC: 18263 AN: 39462

South Asian (SAS) AF: 0.119 AC: 10194 AN: 85512

European-Finnish (FIN) AF: 0.0110 AC: 574 AN: 52330

Middle Eastern (MID) AF: 0.0412 AC: 236 AN: 5734

European-Non Finnish (NFE) AF: 0.0199 AC: 22073 AN: 1106698

Other (OTH) AF: 0.0732 AC: 4395 AN: 60010

GnomAD4 genome AF: 0.105 AC: 15914 AN: 152274 Hom.: 1886 Cov.: 32 AF XY: 0.110 AC XY: 8181 AN XY: 74460

African (AFR) AF: 0.179 AC: 7444 AN: 41538

American (AMR) AF: 0.242 AC: 3694 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3472

East Asian (EAS) AF: 0.468 AC: 2425 AN: 5182

South Asian (SAS) AF: 0.136 AC: 658 AN: 4826

European-Finnish (FIN) AF: 0.0108 AC: 115 AN: 10612

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0182 AC: 1238 AN: 68030

Other (OTH) AF: 0.104 AC: 220 AN: 2114

Alfa AF: 0.0567 Hom.: 1027

Bravo AF: 0.126

Asia WGS AF: 0.265 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.75
PhyloP100		0.28
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: rs2294686; hg19: chr6-24709202;