rs9475671

Variant names:

• chr6-56321645-G-A
• rs9475671
• ENST00000370819.5:c.-39+72326C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-56321645-G-A
• chr6-56321645-G-T

Variant summary

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

The ENST00000370819.5(COL21A1):​c.-39+72326C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,964 control chromosomes in the GnomAD database, including 10,301 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 0.35 (10301 hom., cov: 33)
• Consequence: COL21A1 ENST00000370819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793
• Publications: 0 publications found

Genes affected

COL21A1 (HGNC:17025): (collagen type XXI alpha 1 chain) This gene encodes the alpha chain of type XXI collagen, a member of the FACIT (fibril-associated collagens with interrupted helices) collagen family. Type XXI collagen is localized to tissues containing type I collagen and maintains the integrity of the extracellular matrix. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL21A1	NM_001318752.2	c.-39+72326C>T		intron_variant	Intron 1 of 28		NP_001305681.1
COL21A1	XM_011514924.3	c.-39+72326C>T		intron_variant	Intron 1 of 29		XP_011513226.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL21A1	ENST00000370819.5	c.-39+72326C>T		intron_variant	Intron 1 of 28	1		ENSP00000359855.1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53807 AN: 151842 Hom.: 10293 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.0954

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.354 AC: 53838 AN: 151964 Hom.: 10301 Cov.: 33 AF XY: 0.349 AC XY: 25939 AN XY: 74246

African (AFR) AF: 0.282 AC: 11688 AN: 41468

American (AMR) AF: 0.246 AC: 3758 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1296 AN: 3470

East Asian (EAS) AF: 0.0952 AC: 492 AN: 5168

South Asian (SAS) AF: 0.259 AC: 1248 AN: 4816

European-Finnish (FIN) AF: 0.449 AC: 4720 AN: 10516

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.435 AC: 29596 AN: 67964

Other (OTH) AF: 0.335 AC: 707 AN: 2108

Alfa AF: 0.359 Hom.: 1680

Bravo AF: 0.335

Asia WGS AF: 0.171 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.54
PhyloP100		-0.79
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs9475671; hg19: chr6-56186443;