rs876537

Positions:

• chr1-159705143-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

CRPP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CRPP1		n.159705143C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRPP1	ENST00000412857.1	n.465G>A		non_coding_transcript_exon_variant	1/1	6

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

Gnomad4 AFR exome AF: 0.199

Gnomad4 AMR exome AF: 0.383

Gnomad4 ASJ exome AF: 0.409

Gnomad4 EAS exome AF: 0.599

Gnomad4 SAS exome AF: 0.308

Gnomad4 FIN exome AF: 0.385

Gnomad4 NFE exome AF: 0.381

Gnomad4 OTH exome AF: 0.383

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

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.365

Alfa AF: 0.388 Hom.: 21368

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs876537; hg19: chr1-159674933;