7-94380322-T-C

Variant names:

• chr7-94380322-T-C
• rs7792596
• ENST00000642601.1:n.480A>G

Variant summary

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

The ENST00000642601.1(ENSG00000285090):​n.480A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,094 control chromosomes in the GnomAD database, including 21,313 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 0.48 (21313 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: ENSG00000285090 ENST00000642601.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93
• Publications: 6 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL1A2-AS1	NR_147206.1	n.476A>G		non_coding_transcript_exon_variant	Exon 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285090	ENST00000642601.1	n.480A>G		non_coding_transcript_exon_variant	Exon 5 of 9
ENSG00000285090	ENST00000834103.1	n.273A>G		non_coding_transcript_exon_variant	Exon 3 of 6
ENSG00000285090	ENST00000834107.1	n.443A>G		non_coding_transcript_exon_variant	Exon 5 of 7

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73617 AN: 151968 Hom.: 21261 Cov.: 33

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.467

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 2 AN XY: 8

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

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) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.485 AC: 73727 AN: 152086 Hom.: 21313 Cov.: 33 AF XY: 0.487 AC XY: 36234 AN XY: 74350

African (AFR) AF: 0.763 AC: 31678 AN: 41494

American (AMR) AF: 0.540 AC: 8256 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1102 AN: 3472

East Asian (EAS) AF: 0.894 AC: 4615 AN: 5160

South Asian (SAS) AF: 0.460 AC: 2222 AN: 4826

European-Finnish (FIN) AF: 0.284 AC: 3000 AN: 10572

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21485 AN: 67958

Other (OTH) AF: 0.473 AC: 997 AN: 2110

Alfa AF: 0.379 Hom.: 42334

Bravo AF: 0.519

Asia WGS AF: 0.690 AC: 2398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.13
DANN	Benign	0.68
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs7792596; hg19: chr7-94009634;