rs876537

Variant names:

• chr1-159705143-C-T
• rs876537
• ENST00000412857.1:n.465G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000412857.1(CRPP1):​n.465G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.358 in 241,664 control chromosomes in the GnomAD database, including 16,438 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 0.35 (9827 hom., cov: 32)
  • Exomes 𝑓: 0.38 (6611 hom.)
• Consequence: CRPP1 ENST00000412857.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.01
• Publications: 43 publications found

Genes affected

CRPP1 (HGNC:2368): (C-reactive protein pseudogene 1)

ENSG00000297913 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRPP1		n.159705143C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRPP1	ENST00000412857.1	n.465G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000297913	ENST00000751816.1	n.108-21384C>T		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-21384C>T		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-21384C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52643 AN: 152016 Hom.: 9822 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.353

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.366

GnomAD4 exome AF: 0.379 AC: 33908 AN: 89530 Hom.: 6611 Cov.: 0 AF XY: 0.378 AC XY: 19644 AN XY: 52024

African (AFR) AF: 0.199 AC: 425 AN: 2136

American (AMR) AF: 0.383 AC: 3853 AN: 10072

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 582 AN: 1422

East Asian (EAS) AF: 0.599 AC: 2597 AN: 4334

South Asian (SAS) AF: 0.308 AC: 3498 AN: 11354

European-Finnish (FIN) AF: 0.385 AC: 2335 AN: 6072

Middle Eastern (MID) AF: 0.379 AC: 639 AN: 1684

European-Non Finnish (NFE) AF: 0.381 AC: 18446 AN: 48450

Other (OTH) AF: 0.383 AC: 1533 AN: 4006

GnomAD4 genome AF: 0.346 AC: 52664 AN: 152134 Hom.: 9827 Cov.: 32 AF XY: 0.348 AC XY: 25898 AN XY: 74374

African (AFR) AF: 0.209 AC: 8662 AN: 41510

American (AMR) AF: 0.406 AC: 6218 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1326 AN: 3468

East Asian (EAS) AF: 0.576 AC: 2973 AN: 5164

South Asian (SAS) AF: 0.338 AC: 1632 AN: 4822

European-Finnish (FIN) AF: 0.390 AC: 4129 AN: 10586

Middle Eastern (MID) AF: 0.348 AC: 101 AN: 290

European-Non Finnish (NFE) AF: 0.389 AC: 26431 AN: 67972

Other (OTH) AF: 0.365 AC: 771 AN: 2114

Alfa AF: 0.379 Hom.: 42660

Bravo AF: 0.341

Asia WGS AF: 0.444 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	11
DANN	Benign	0.75
PhyloP100		4.0

Splicing

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

Other links and lift over

dbSNP: rs876537; hg19: chr1-159674933;