rs6970279

Variant names:

• chr7-94385577-C-A
• rs6970279
• ENST00000642601.1:n.328-37G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-94385577-C-A
• chr7-94385577-C-T

Variant summary

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

The ENST00000642601.1(ENSG00000285090):​n.328-37G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 150,004 control chromosomes in the GnomAD database, including 7,528 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 0.31 (7528 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000285090 ENST00000642601.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.982
• Publications: 5 publications found

Genes affected

ENSG00000285090 (HGNC:):

COL1A2-AS1 (HGNC:53133): (COL1A2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL1A2-AS1	NR_147206.1	n.324-37G>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285090	ENST00000642601.1	n.328-37G>T		intron_variant	Intron 3 of 8
ENSG00000285090	ENST00000644739.2	n.252+5828G>T		intron_variant	Intron 3 of 5
ENSG00000285090	ENST00000834100.1	n.211+5828G>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.313 AC: 46850 AN: 149890 Hom.: 7512 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.318

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.313 AC: 46898 AN: 150004 Hom.: 7528 Cov.: 32 AF XY: 0.314 AC XY: 22987 AN XY: 73264

African (AFR) AF: 0.374 AC: 14943 AN: 39908

American (AMR) AF: 0.418 AC: 6354 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 969 AN: 3466

East Asian (EAS) AF: 0.397 AC: 1931 AN: 4866

South Asian (SAS) AF: 0.280 AC: 1327 AN: 4738

European-Finnish (FIN) AF: 0.211 AC: 2230 AN: 10556

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18172 AN: 67968

Other (OTH) AF: 0.318 AC: 665 AN: 2088

Alfa AF: 0.305 Hom.: 3213

Bravo AF: 0.325

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.8
DANN	Benign	0.66
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs6970279; hg19: chr7-94014889;