20-32031543-T-A

Variant names:

• chr20-32031543-T-A
• rs6121315
• NM_001365692.1:c.*229T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001365692.1(CCM2L):​c.*229T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CCM2L NM_001365692.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.27
• Publications: 3 publications found

Genes affected

CCM2L (HGNC:16153): (CCM2 like scaffold protein) Predicted to act upstream of or within several processes, including heart development; negative regulation of homotypic cell-cell adhesion; and positive regulation of fibroblast growth factor production. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000226239 (HGNC:58356):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001365692.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCM2L	NM_001365692.1	MANE Select	c.*229T>A		3_prime_UTR	Exon 10 of 10	NP_001352621.1
	CCM2L	NM_080625.4		c.*579T>A		3_prime_UTR	Exon 9 of 9	NP_542192.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCM2L	ENST00000452892.3	TSL:2 MANE Select	c.*229T>A		3_prime_UTR	Exon 10 of 10	ENSP00000392448.2
	CCM2L	ENST00000262659.12	TSL:1	c.*579T>A		3_prime_UTR	Exon 9 of 9	ENSP00000262659.8
	ENSG00000226239	ENST00000449519.1	TSL:2	n.33A>T		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 150170 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 81366

African (AFR) AF: 0.00 AC: 0 AN: 1676

American (AMR) AF: 0.00 AC: 0 AN: 4356

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3162

East Asian (EAS) AF: 0.00 AC: 0 AN: 3316

South Asian (SAS) AF: 0.00 AC: 0 AN: 29576

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8178

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 550

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 91902

Other (OTH) AF: 0.00 AC: 0 AN: 7454

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 2100

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.60
PhyloP100		-3.3

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: rs6121315; hg19: chr20-30619346;