6-24712916-A-C

Position:

• chr6-24712916-A-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.84).
• 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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 20 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C6orf62	NM_030939.5	c.429+1402T>G		intron_variant		ENST00000378119.9
C6orf62	NM_001410835.1	c.342+1402T>G		intron_variant
C6orf62	XM_005249433.5	c.429+1402T>G		intron_variant
C6orf62	XM_047419384.1	c.342+1402T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C6orf62	ENST00000378119.9	c.429+1402T>G		intron_variant		1	NM_030939.5	P1
C6orf62	ENST00000378102.3	c.342+1402T>G		intron_variant		5
C6orf62	ENST00000710317.1	c.429+1402T>G		intron_variant				P1

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

Gnomad4 AFR AF: 0.0329

Gnomad4 AMR AF: 0.00353

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.000831

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000279

Gnomad4 OTH AF: 0.0123

Alfa AF: 0.00420 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

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: rs6913673; hg19: chr6-24713144;