1-159705143-C-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412857.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRPP1	ENST00000412857.1	TSL:6	n.465G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000297913	ENST00000751816.1		n.108-21384C>T		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-21384C>T		intron	N/A

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 v4.9

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;