NM_152888.3:c.1902+1770T>G

Variant names:

• chr8-138758473-A-C
• rs7824025
• NM_152888.3:c.1902+1770T>G

Variant summary

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

The NM_152888.3(COL22A1):​c.1902+1770T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 152,218 control chromosomes in the GnomAD database, including 62,603 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 0.91 (62603 hom., cov: 33)
• Consequence: COL22A1 NM_152888.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 3 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL22A1	NM_152888.3	c.1902+1770T>G		intron_variant	Intron 18 of 64	ENST00000303045.11	NP_690848.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL22A1	ENST00000303045.11	c.1902+1770T>G		intron_variant	Intron 18 of 64	1	NM_152888.3	ENSP00000303153.6

Frequencies

GnomAD3 genomes AF: 0.906 AC: 137856 AN: 152100 Hom.: 62570 Cov.: 33

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.835

Gnomad AMR AF: 0.939

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.913

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.910

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

GnomAD4 genome AF: 0.906 AC: 137942 AN: 152218 Hom.: 62603 Cov.: 33 AF XY: 0.911 AC XY: 67827 AN XY: 74428

African (AFR) AF: 0.866 AC: 35956 AN: 41524

American (AMR) AF: 0.939 AC: 14379 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.932 AC: 3237 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5143 AN: 5172

South Asian (SAS) AF: 0.939 AC: 4524 AN: 4820

European-Finnish (FIN) AF: 0.965 AC: 10230 AN: 10606

Middle Eastern (MID) AF: 0.910 AC: 264 AN: 290

European-Non Finnish (NFE) AF: 0.905 AC: 61534 AN: 68012

Other (OTH) AF: 0.909 AC: 1915 AN: 2106

Alfa AF: 0.909 Hom.: 116606

Bravo AF: 0.904

Asia WGS AF: 0.954 AC: 3319 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	1.5
DANN	Benign	0.45
PhyloP100		-0.59
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: rs7824025; hg19: chr8-139770716;