rs6913673

Variant names:

• chr6-24712916-A-C
• rs6913673
• NM_030939.5:c.429+1402T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_030939.5(C6orf62):​c.429+1402T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00971 in 152,180 control chromosomes in the GnomAD database, including 20 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 0.0097 (20 hom., cov: 32)
• Consequence: C6orf62 NM_030939.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523
• Publications: 0 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=-0.84).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00971 (1478/152180) while in subpopulation AFR AF = 0.0329 (1364/41512). AF 95% confidence interval is 0.0314. There are 20 homozygotes in GnomAd4. There are 694 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 20 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C6orf62	NM_030939.5	c.429+1402T>G		intron_variant	Intron 3 of 4	ENST00000378119.9	NP_112201.1
C6orf62	NM_001410835.1	c.342+1402T>G		intron_variant	Intron 3 of 4		NP_001397764.1
C6orf62	XM_005249433.5	c.429+1402T>G		intron_variant	Intron 3 of 3		XP_005249490.1
C6orf62	XM_047419384.1	c.342+1402T>G		intron_variant	Intron 3 of 3		XP_047275340.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C6orf62	ENST00000378119.9	c.429+1402T>G		intron_variant	Intron 3 of 4	1	NM_030939.5	ENSP00000367359.4
C6orf62	ENST00000710317.1	c.429+1402T>G		intron_variant	Intron 3 of 4			ENSP00000518198.1
C6orf62	ENST00000378102.3	c.342+1402T>G		intron_variant	Intron 3 of 4	5		ENSP00000367342.3

Frequencies

GnomAD3 genomes AF: 0.00972 AC: 1478 AN: 152064 Hom.: 20 Cov.: 32

Gnomad AFR AF: 0.0330

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00354

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.000830

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000279

Gnomad OTH AF: 0.0124

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00971 AC: 1478 AN: 152180 Hom.: 20 Cov.: 32 AF XY: 0.00933 AC XY: 694 AN XY: 74414

African (AFR) AF: 0.0329 AC: 1364 AN: 41512

American (AMR) AF: 0.00353 AC: 54 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.000831 AC: 4 AN: 4814

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10606

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.000279 AC: 19 AN: 67998

Other (OTH) AF: 0.0123 AC: 26 AN: 2112

Alfa AF: 0.00510 Hom.: 3

Bravo AF: 0.0118

Asia WGS AF: 0.00202 AC: 8 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.76
DANN	Benign	0.35
PhyloP100		-0.52
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: rs6913673; hg19: chr6-24713144;