rs1529711

Positions:

• chr19-10912758-C-T

Variant summary

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

The NM_199141.2(CARM1):​c.669+464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,066 control chromosomes in the GnomAD database, including 1,308 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 0.12 (1308 hom., cov: 31)
• Consequence: CARM1 NM_199141.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

Genes affected

CARM1 (HGNC:23393): (coactivator associated arginine methyltransferase 1) This gene belongs to the protein arginine methyltransferase (PRMT) family. The encoded enzyme catalyzes the methylation of guanidino nitrogens of arginyl residues of proteins. The enzyme acts specifically on histones and other chromatin-associated proteins and is involved in regulation of gene expression. The enzyme may act in association with other proteins or within multi-protein complexes and may play a role in cell type-specific functions and cell lineage specification. A related pseudogene is located on chromosome 9. [provided by RefSeq, Aug 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CARM1	NM_199141.2	c.669+464C>T		intron_variant		ENST00000327064.9	NP_954592.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CARM1	ENST00000327064.9	c.669+464C>T		intron_variant		1	NM_199141.2	ENSP00000325690.4

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18802 AN: 151948 Hom.: 1307 Cov.: 31

Gnomad AFR AF: 0.0817

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0953

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.0251

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.124 AC: 18809 AN: 152066 Hom.: 1308 Cov.: 31 AF XY: 0.124 AC XY: 9210 AN XY: 74334

Gnomad4 AFR AF: 0.0815

Gnomad4 AMR AF: 0.0953

Gnomad4 ASJ AF: 0.0903

Gnomad4 EAS AF: 0.0254

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.122

Alfa AF: 0.139 Hom.: 2047

Bravo AF: 0.113

Asia WGS AF: 0.0810 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.68
DANN	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs1529711; hg19: chr19-11023434;