rs4013197

Variant names:

• chr9-2921825-G-A
• rs4013197
• ENST00000426329.6:n.828C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-2921825-G-A
• chr9-2921825-G-T

Variant summary

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

The ENST00000426329.6(CARM1P1):​n.828C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.378 in 147,330 control chromosomes in the GnomAD database, including 12,185 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 0.40 (11816 hom., cov: 29)
  • Exomes 𝑓: 0.22 (369 hom.)
• Consequence: CARM1P1 ENST00000426329.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.43
• Publications: 4 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=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CARM1P1	ENST00000426329.6	n.828C>T		non_coding_transcript_exon_variant	Exon 8 of 11	6
ENSG00000290482	ENST00000497195.2	n.913C>T		non_coding_transcript_exon_variant	Exon 7 of 8	2
ENSG00000290482	ENST00000515723.2	n.1395C>T		non_coding_transcript_exon_variant	Exon 11 of 12	5

Frequencies

GnomAD3 genomes AF: 0.395 AC: 52315 AN: 132366 Hom.: 11765 Cov.: 29

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.0361

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.371

GnomAD4 exome AF: 0.221 AC: 3278 AN: 14850 Hom.: 369 Cov.: 0 AF XY: 0.221 AC XY: 1556 AN XY: 7056

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.221 AC: 3231 AN: 14652

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.250 AC: 23 AN: 92

Other (OTH) AF: 0.228 AC: 21 AN: 92

GnomAD4 genome AF: 0.396 AC: 52420 AN: 132480 Hom.: 11816 Cov.: 29 AF XY: 0.392 AC XY: 25417 AN XY: 64794

African (AFR) AF: 0.699 AC: 27335 AN: 39082

American (AMR) AF: 0.265 AC: 3350 AN: 12662

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 958 AN: 2982

East Asian (EAS) AF: 0.0359 AC: 139 AN: 3870

South Asian (SAS) AF: 0.344 AC: 1439 AN: 4186

European-Finnish (FIN) AF: 0.254 AC: 2380 AN: 9378

Middle Eastern (MID) AF: 0.368 AC: 86 AN: 234

European-Non Finnish (NFE) AF: 0.277 AC: 15989 AN: 57626

Other (OTH) AF: 0.369 AC: 651 AN: 1762

Alfa AF: 0.306 Hom.: 6104

Bravo AF: 0.374

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	8.5
DANN	Benign	0.72
PhyloP100		4.4

Splicing

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

Other links and lift over

dbSNP: rs4013197; hg19: chr9-2921825;