chr6-31112655-A-G

Variant names:

• chr6-31112655-A-G
• rs2233969
• NM_014070.3:c.-100T>C

Variant summary

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

The NM_014070.3(C6orf15):​c.-100T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 762,804 control chromosomes in the GnomAD database, including 15,157 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 0.16 (2236 hom., cov: 33)
  • Exomes 𝑓: 0.20 (12921 hom.)
• Consequence: C6orf15 NM_014070.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 12 publications found

Genes affected

C6orf15 (HGNC:13927): (chromosome 6 open reading frame 15) Predicted to enable several functions, including collagen V binding activity; fibronectin binding activity; and glycosaminoglycan binding activity. Predicted to be involved in extracellular matrix organization. Predicted to be located in interstitial matrix. Predicted to be active in extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C6orf15	NM_014070.3	c.-100T>C		upstream_gene_variant		ENST00000259870.4	NP_054789.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C6orf15	ENST00000259870.4	c.-100T>C		upstream_gene_variant		1	NM_014070.3	ENSP00000259870.3

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24414 AN: 152134 Hom.: 2239 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.160

GnomAD4 exome AF: 0.195 AC: 119182 AN: 610552 Hom.: 12921 AF XY: 0.199 AC XY: 61989 AN XY: 311206

African (AFR) AF: 0.102 AC: 1518 AN: 14870

American (AMR) AF: 0.180 AC: 2793 AN: 15510

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 2075 AN: 14076

East Asian (EAS) AF: 0.389 AC: 11523 AN: 29606

South Asian (SAS) AF: 0.289 AC: 12817 AN: 44370

European-Finnish (FIN) AF: 0.140 AC: 5527 AN: 39344

Middle Eastern (MID) AF: 0.248 AC: 969 AN: 3900

European-Non Finnish (NFE) AF: 0.183 AC: 76342 AN: 418298

Other (OTH) AF: 0.184 AC: 5618 AN: 30578

GnomAD4 genome AF: 0.160 AC: 24423 AN: 152252 Hom.: 2236 Cov.: 33 AF XY: 0.162 AC XY: 12026 AN XY: 74442

African (AFR) AF: 0.103 AC: 4286 AN: 41546

American (AMR) AF: 0.164 AC: 2511 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1907 AN: 5180

South Asian (SAS) AF: 0.276 AC: 1330 AN: 4826

European-Finnish (FIN) AF: 0.140 AC: 1488 AN: 10612

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11855 AN: 67998

Other (OTH) AF: 0.160 AC: 339 AN: 2116

Alfa AF: 0.180 Hom.: 5429

Bravo AF: 0.156

Asia WGS AF: 0.281 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.81
PhyloP100		-0.22
PromoterAI		0.017	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2233969; hg19: chr6-31080432;