rs7045640

Variant names:

• chr9-2978377-A-C
• rs7045640

Variant summary

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

The variant allele was found at a frequency of 0.0755 in 152,240 control chromosomes in the GnomAD database, including 1,288 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 0.076 (1288 hom., cov: 33)
• Consequence: CARM1P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.855
• Publications: 1 publications found

Genes affected

CARM1P1 (HGNC:23392): (coactivator associated arginine methyltransferase 1 pseudogene 1)

ENSG00000290482 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARM1P1		n.2978377A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CARM1P1	ENST00000426329.6	n.427+14086T>G		intron_variant	Intron 4 of 10	6
ENSG00000290482	ENST00000497195.2	n.512+13657T>G		intron_variant	Intron 3 of 7	2
ENSG00000290482	ENST00000515723.2	n.994+13657T>G		intron_variant	Intron 7 of 11	5

Frequencies

GnomAD3 genomes AF: 0.0754 AC: 11471 AN: 152122 Hom.: 1286 Cov.: 33

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0349

Gnomad ASJ AF: 0.00721

Gnomad EAS AF: 0.00750

Gnomad SAS AF: 0.00641

Gnomad FIN AF: 0.00405

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00831

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0755 AC: 11498 AN: 152240 Hom.: 1288 Cov.: 33 AF XY: 0.0732 AC XY: 5449 AN XY: 74452

African (AFR) AF: 0.244 AC: 10124 AN: 41504

American (AMR) AF: 0.0348 AC: 533 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00721 AC: 25 AN: 3468

East Asian (EAS) AF: 0.00732 AC: 38 AN: 5188

South Asian (SAS) AF: 0.00663 AC: 32 AN: 4830

European-Finnish (FIN) AF: 0.00405 AC: 43 AN: 10624

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00829 AC: 564 AN: 68010

Other (OTH) AF: 0.0620 AC: 131 AN: 2112

Alfa AF: 0.0275 Hom.: 263

Bravo AF: 0.0861

Asia WGS AF: 0.0280 AC: 97 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.5
DANN	Benign	0.88
PhyloP100		0.85

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7045640; hg19: chr9-2978377;