rs3813687

Variant names:

• chr6-24719750-G-A
• rs3813687
• ENST00000710317.1:c.-1082C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-24719750-G-A
• chr6-24719750-G-T

Variant summary

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

The ENST00000710317.1(C6orf62):​c.-1082C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,539,796 control chromosomes in the GnomAD database, including 24,754 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 0.13 (1632 hom., cov: 31)
  • Exomes 𝑓: 0.18 (23122 hom.)
• Consequence: C6orf62 ENST00000710317.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337
• Publications: 15 publications found

Genes affected

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

ENSG00000288851 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C6orf62	NM_001410835.1	c.42+110C>T		intron_variant	Intron 1 of 4		NP_001397764.1
C6orf62	XM_047419384.1	c.42+110C>T		intron_variant	Intron 1 of 3		XP_047275340.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C6orf62	ENST00000710317.1	c.-1082C>T		5_prime_UTR_variant	Exon 1 of 5			ENSP00000518198.1
C6orf62	ENST00000378102.3	c.42+110C>T		intron_variant	Intron 1 of 4	5		ENSP00000367342.3
ENSG00000288851	ENST00000809709.1	n.-83G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19930 AN: 151924 Hom.: 1633 Cov.: 31

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.100

GnomAD4 exome AF: 0.178 AC: 246753 AN: 1387752 Hom.: 23122 Cov.: 41 AF XY: 0.175 AC XY: 119798 AN XY: 684134

African (AFR) AF: 0.0266 AC: 834 AN: 31402

American (AMR) AF: 0.147 AC: 5138 AN: 34838

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 3965 AN: 24464

East Asian (EAS) AF: 0.121 AC: 4305 AN: 35564

South Asian (SAS) AF: 0.106 AC: 8241 AN: 78110

European-Finnish (FIN) AF: 0.195 AC: 9252 AN: 47524

Middle Eastern (MID) AF: 0.101 AC: 419 AN: 4142

European-Non Finnish (NFE) AF: 0.191 AC: 205487 AN: 1074202

Other (OTH) AF: 0.158 AC: 9112 AN: 57506

GnomAD4 genome AF: 0.131 AC: 19927 AN: 152044 Hom.: 1632 Cov.: 31 AF XY: 0.131 AC XY: 9721 AN XY: 74312

African (AFR) AF: 0.0320 AC: 1327 AN: 41514

American (AMR) AF: 0.133 AC: 2031 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 548 AN: 3466

East Asian (EAS) AF: 0.120 AC: 618 AN: 5160

South Asian (SAS) AF: 0.0979 AC: 473 AN: 4830

European-Finnish (FIN) AF: 0.198 AC: 2085 AN: 10542

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12423 AN: 67964

Other (OTH) AF: 0.0992 AC: 208 AN: 2096

Alfa AF: 0.164 Hom.: 3624

Bravo AF: 0.125

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	16
DANN	Benign	0.83
PhyloP100		0.34
PromoterAI		0.064	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=300/0	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: rs3813687; hg19: chr6-24719978;