rs1858823

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_147206.1(COL1A2-AS1):​n.323+1700C>T variant causes a intron, non coding transcript 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: COL1A2-AS1 NR_147206.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
COL1A2-AS1	NR_147206.1	n.323+1700C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000642601.1	n.327+1700C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.471

Alfa AF: 0.152 Hom.: 240

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1858823; hg19: chr7-94018240;