chr7-66152608-T-C

Position:

• chr7-66152608-T-C

Variant summary

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

The NM_014478.5(CRCP):​c.*251T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 454,970 control chromosomes in the GnomAD database, including 74,740 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 0.59 (27143 hom., cov: 31)
  • Exomes 𝑓: 0.55 (47597 hom.)
• Consequence: CRCP NM_014478.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514

Genes affected

CRCP (HGNC:17888): (CGRP receptor component) This gene encodes a membrane protein that functions as part of a receptor complex for a small neuropeptide that increases intracellular cAMP levels. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

CRCP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRCP	NM_014478.5	c.*251T>C		3_prime_UTR_variant	6/6	ENST00000395326.8	NP_055293.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRCP	ENST00000395326.8	c.*251T>C		3_prime_UTR_variant	6/6	1	NM_014478.5	ENSP00000378736.3

Frequencies

GnomAD3 genomes AF: 0.593 AC: 89982 AN: 151860 Hom.: 27114 Cov.: 31

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.571

GnomAD4 exome AF: 0.554 AC: 167976 AN: 302992 Hom.: 47597 Cov.: 4 AF XY: 0.548 AC XY: 88043 AN XY: 160538

Gnomad4 AFR exome AF: 0.686

Gnomad4 AMR exome AF: 0.549

Gnomad4 ASJ exome AF: 0.573

Gnomad4 EAS exome AF: 0.327

Gnomad4 SAS exome AF: 0.481

Gnomad4 FIN exome AF: 0.557

Gnomad4 NFE exome AF: 0.585

Gnomad4 OTH exome AF: 0.561

GnomAD4 genome AF: 0.593 AC: 90063 AN: 151978 Hom.: 27143 Cov.: 31 AF XY: 0.589 AC XY: 43709 AN XY: 74262

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.570

Alfa AF: 0.564 Hom.: 33636

Bravo AF: 0.595

Asia WGS AF: 0.390 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.3
DANN	Benign	0.65
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs875971; hg19: chr7-65617595;