chr7-94377682-C-T

Variant names:

• chr7-94377682-C-T
• rs13221576
• ENST00000642601.1:n.495+2625G>A

Variant summary

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

The NR_147206.1(COL1A2-AS1):​n.491+2625G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,220 control chromosomes in the GnomAD database, including 1,626 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 0.14 (1626 hom., cov: 32)
• Consequence: COL1A2-AS1 NR_147206.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_147206.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL1A2-AS1	NR_147206.1		n.491+2625G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285090	ENST00000642601.1		n.495+2625G>A		intron	N/A
	ENSG00000285090	ENST00000644739.2		n.252+13723G>A		intron	N/A
	ENSG00000285090	ENST00000834100.1		n.211+13723G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20869 AN: 152100 Hom.: 1613 Cov.: 32

Gnomad AFR AF: 0.0800

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0777

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0895

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.137 AC: 20904 AN: 152220 Hom.: 1626 Cov.: 32 AF XY: 0.136 AC XY: 10148 AN XY: 74422

African (AFR) AF: 0.0803 AC: 3334 AN: 41540

American (AMR) AF: 0.256 AC: 3910 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 642 AN: 3472

East Asian (EAS) AF: 0.0777 AC: 403 AN: 5188

South Asian (SAS) AF: 0.106 AC: 510 AN: 4822

European-Finnish (FIN) AF: 0.0895 AC: 948 AN: 10594

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10607 AN: 68000

Other (OTH) AF: 0.159 AC: 336 AN: 2114

Alfa AF: 0.150 Hom.: 4815

Bravo AF: 0.146

Asia WGS AF: 0.103 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.41
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs13221576; hg19: chr7-94006994;