rs7839680

Variant names:

• chr8-138681438-G-A
• rs7839680
• NM_152888.3:c.3013-1762C>T

Variant summary

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

The NM_152888.3(COL22A1):​c.3013-1762C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,046 control chromosomes in the GnomAD database, including 2,604 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 0.19 (2604 hom., cov: 31)
• Consequence: COL22A1 NM_152888.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835
• Publications: 4 publications found

Genes affected

COL22A1 (HGNC:22989): (collagen type XXII alpha 1 chain) This gene encodes member of the collagen family which is thought to contribute to the stabilization of myotendinous junctions and strengthen skeletal muscle attachments during contractile activity. It belongs to the fibril-associated collagens with interrupted triple helix (FACIT) subset of the collagen superfamily, which associate with collagen fibers through their C-terminal collagenous domains and mediate protein-protein interactions through their N-terminal noncollagenous domains. The encoded protein is deposited in the basement membrane zone of the myotendinous junction which is present only at the tissue junctions of muscles, tendons, the heart, articular cartilage, and skin. A knockdown of the orthologous zebrafish gene induces a muscular dystrophy by disruption of the myotendinous junction. [provided by RefSeq, May 2017]

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 (SAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL22A1	NM_152888.3	c.3013-1762C>T		intron_variant	Intron 39 of 64	ENST00000303045.11	NP_690848.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL22A1	ENST00000303045.11	c.3013-1762C>T		intron_variant	Intron 39 of 64	1	NM_152888.3	ENSP00000303153.6
COL22A1	ENST00000341807.8	n.757+2987C>T		intron_variant	Intron 14 of 38	1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28174 AN: 151930 Hom.: 2603 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.185 AC: 28191 AN: 152046 Hom.: 2604 Cov.: 31 AF XY: 0.189 AC XY: 14033 AN XY: 74306

African (AFR) AF: 0.194 AC: 8061 AN: 41476

American (AMR) AF: 0.201 AC: 3069 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3468

East Asian (EAS) AF: 0.172 AC: 887 AN: 5170

South Asian (SAS) AF: 0.212 AC: 1019 AN: 4810

European-Finnish (FIN) AF: 0.222 AC: 2346 AN: 10576

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.175 AC: 11920 AN: 67954

Other (OTH) AF: 0.193 AC: 407 AN: 2112

Alfa AF: 0.176 Hom.: 7731

Bravo AF: 0.183

Asia WGS AF: 0.199 AC: 692 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	0.57
DANN	Benign	0.18
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7839680; hg19: chr8-139693681;