rs1529711

Variant names:

• chr19-10912758-C-T
• rs1529711
• NM_199141.2:c.669+464C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CARM1	NM_199141.2	c.669+464C>T		intron_variant	Intron 5 of 15	ENST00000327064.9	NP_954592.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CARM1	ENST00000327064.9	c.669+464C>T		intron_variant	Intron 5 of 15	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

African (AFR) AF: 0.0815 AC: 3382 AN: 41484

American (AMR) AF: 0.0953 AC: 1455 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0903 AC: 313 AN: 3468

East Asian (EAS) AF: 0.0254 AC: 131 AN: 5162

South Asian (SAS) AF: 0.108 AC: 519 AN: 4822

European-Finnish (FIN) AF: 0.216 AC: 2291 AN: 10596

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.153 AC: 10369 AN: 67952

Other (OTH) AF: 0.122 AC: 257 AN: 2112

Alfa AF: 0.136 Hom.: 2722

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
PhyloP100		-0.64
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: rs1529711; hg19: chr19-11023434;