chr19-10891903-A-G

Position:

• chr19-10891903-A-G

Variant summary

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

The NM_199141.2(CARM1):​c.221-13048A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 152,306 control chromosomes in the GnomAD database, including 63,202 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 (63202 hom., cov: 32)
• Consequence: CARM1 NM_199141.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CARM1	NM_199141.2	c.221-13048A>G		intron_variant		ENST00000327064.9	NP_954592.1
CARM1	NM_001370088.1	c.221-13048A>G		intron_variant			NP_001357017.1
CARM1	NM_001370089.1	c.116-13048A>G		intron_variant			NP_001357018.1
CARM1	XM_047438058.1	c.116-13048A>G		intron_variant			XP_047294014.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CARM1	ENST00000327064.9	c.221-13048A>G		intron_variant		1	NM_199141.2	ENSP00000325690.4

Frequencies

GnomAD3 genomes AF: 0.909 AC: 138359 AN: 152188 Hom.: 63137 Cov.: 32

Gnomad AFR AF: 0.978

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.909 AC: 138484 AN: 152306 Hom.: 63202 Cov.: 32 AF XY: 0.911 AC XY: 67854 AN XY: 74474

Gnomad4 AFR AF: 0.978

Gnomad4 AMR AF: 0.933

Gnomad4 ASJ AF: 0.852

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.962

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.908

Alfa AF: 0.806 Hom.: 2630

Bravo AF: 0.917

Asia WGS AF: 0.982 AC: 3415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.79
DANN	Benign	0.53

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: rs7254708; hg19: chr19-11002579;