rs1858823

Variant names:

• chr7-94388928-G-A
• rs1858823
• ENST00000642601.1:n.327+1700C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-94388928-G-A
• chr7-94388928-G-C
• chr7-94388928-G-T

Variant summary

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

The ENST00000642601.1(ENSG00000285090):​n.327+1700C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,896 control chromosomes in the GnomAD database, including 20,969 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 (20969 hom., cov: 32)
• Consequence: ENSG00000285090 ENST00000642601.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 2 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL1A2-AS1	NR_147206.1	n.323+1700C>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285090	ENST00000642601.1	n.327+1700C>T		intron_variant	Intron 3 of 8
ENSG00000285090	ENST00000644739.2	n.252+2477C>T		intron_variant	Intron 3 of 5
ENSG00000285090	ENST00000834100.1	n.211+2477C>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73074 AN: 151778 Hom.: 20917 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.482 AC: 73185 AN: 151896 Hom.: 20969 Cov.: 32 AF XY: 0.484 AC XY: 35973 AN XY: 74252

African (AFR) AF: 0.758 AC: 31393 AN: 41390

American (AMR) AF: 0.530 AC: 8094 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3470

East Asian (EAS) AF: 0.889 AC: 4601 AN: 5174

South Asian (SAS) AF: 0.459 AC: 2211 AN: 4814

European-Finnish (FIN) AF: 0.285 AC: 3001 AN: 10542

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.316 AC: 21448 AN: 67944

Other (OTH) AF: 0.471 AC: 990 AN: 2102

Alfa AF: 0.195 Hom.: 457

Bravo AF: 0.514

Asia WGS AF: 0.684 AC: 2375 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1858823; hg19: chr7-94018240;