chr19-10911483-T-C

Variant names:

• chr19-10911483-T-C
• rs17616105
• NM_199141.2:c.559-701T>C

Variant summary

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

The NM_199141.2(CARM1):​c.559-701T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,162 control chromosomes in the GnomAD database, including 3,763 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 0.22 (3763 hom., cov: 32)
• Consequence: CARM1 NM_199141.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 8 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARM1	NM_199141.2	c.559-701T>C		intron_variant	Intron 4 of 15	ENST00000327064.9	NP_954592.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CARM1	ENST00000327064.9	c.559-701T>C		intron_variant	Intron 4 of 15	1	NM_199141.2	ENSP00000325690.4

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32705 AN: 152044 Hom.: 3760 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.215 AC: 32718 AN: 152162 Hom.: 3763 Cov.: 32 AF XY: 0.214 AC XY: 15932 AN XY: 74382

African (AFR) AF: 0.131 AC: 5426 AN: 41502

American (AMR) AF: 0.181 AC: 2775 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 928 AN: 3472

East Asian (EAS) AF: 0.179 AC: 927 AN: 5182

South Asian (SAS) AF: 0.251 AC: 1212 AN: 4830

European-Finnish (FIN) AF: 0.231 AC: 2450 AN: 10598

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18153 AN: 67974

Other (OTH) AF: 0.213 AC: 450 AN: 2108

Alfa AF: 0.222 Hom.: 486

Bravo AF: 0.208

Asia WGS AF: 0.193 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.36
PhyloP100		-0.10
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: rs17616105; hg19: chr19-11022159;