rs3734852

Variant names:

• chr6-31111027-G-A
• rs3734852
• NM_014070.3:c.*354C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-31111027-G-A
• chr6-31111027-G-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.*354C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,122 control chromosomes in the GnomAD database, including 1,335 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 (1335 hom., cov: 33)
• Consequence: C6orf15 NM_014070.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 11 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C6orf15	NM_014070.3	c.*354C>T		downstream_gene_variant		ENST00000259870.4	NP_054789.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C6orf15	ENST00000259870.4	c.*354C>T		downstream_gene_variant		1	NM_014070.3	ENSP00000259870.3

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19287 AN: 152006 Hom.: 1328 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.127 AC: 19308 AN: 152122 Hom.: 1335 Cov.: 33 AF XY: 0.127 AC XY: 9479 AN XY: 74372

African (AFR) AF: 0.174 AC: 7216 AN: 41452

American (AMR) AF: 0.0864 AC: 1321 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3472

East Asian (EAS) AF: 0.170 AC: 879 AN: 5160

South Asian (SAS) AF: 0.138 AC: 664 AN: 4822

European-Finnish (FIN) AF: 0.0988 AC: 1048 AN: 10604

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.105 AC: 7145 AN: 68010

Other (OTH) AF: 0.129 AC: 273 AN: 2114

Alfa AF: 0.130 Hom.: 764

Bravo AF: 0.130

Asia WGS AF: 0.142 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.7
DANN	Benign	0.51
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs3734852; hg19: chr6-31078804;