rs7045640

Positions:

• chr9-2978377-A-C

Variant summary

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

The ENST00000426329.6(CARM1P1):​n.427+14086T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 ENST00000426329.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.855

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CARM1P1	ENST00000426329.6	n.427+14086T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.0348

Gnomad4 ASJ AF: 0.00721

Gnomad4 EAS AF: 0.00732

Gnomad4 SAS AF: 0.00663

Gnomad4 FIN AF: 0.00405

Gnomad4 NFE AF: 0.00829

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0249 Hom.: 199

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7045640; hg19: chr9-2978377;