7-66152608-T-C

Variant names:

• chr7-66152608-T-C
• rs875971
• NM_014478.5:c.*251T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 32 publications found

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]

ENSG00000234185 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014478.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRCP	NM_014478.5	MANE Select	c.*251T>C		3_prime_UTR	Exon 6 of 6	NP_055293.1
	CRCP	NM_001142414.1		c.*251T>C		3_prime_UTR	Exon 5 of 5	NP_001135886.1
	CRCP	NM_001040647.2		c.*251T>C		3_prime_UTR	Exon 5 of 5	NP_001035737.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRCP	ENST00000395326.8	TSL:1 MANE Select	c.*251T>C		3_prime_UTR	Exon 6 of 6	ENSP00000378736.3
	CRCP	ENST00000338592.5	TSL:1	c.*251T>C		3_prime_UTR	Exon 5 of 5	ENSP00000340044.5
	CRCP	ENST00000360415.7	TSL:1	n.*691T>C		non_coding_transcript_exon	Exon 7 of 7	ENSP00000353589.3

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

African (AFR) AF: 0.686 AC: 6092 AN: 8876

American (AMR) AF: 0.549 AC: 7160 AN: 13038

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 5341 AN: 9324

East Asian (EAS) AF: 0.327 AC: 5867 AN: 17946

South Asian (SAS) AF: 0.481 AC: 18704 AN: 38910

European-Finnish (FIN) AF: 0.557 AC: 8726 AN: 15666

Middle Eastern (MID) AF: 0.495 AC: 644 AN: 1300

European-Non Finnish (NFE) AF: 0.585 AC: 105791 AN: 180724

Other (OTH) AF: 0.561 AC: 9651 AN: 17208

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

African (AFR) AF: 0.682 AC: 28264 AN: 41456

American (AMR) AF: 0.562 AC: 8582 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1982 AN: 3472

East Asian (EAS) AF: 0.309 AC: 1597 AN: 5162

South Asian (SAS) AF: 0.454 AC: 2185 AN: 4816

European-Finnish (FIN) AF: 0.559 AC: 5896 AN: 10548

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.586 AC: 39797 AN: 67950

Other (OTH) AF: 0.570 AC: 1204 AN: 2112

Alfa AF: 0.575 Hom.: 56698

Bravo AF: 0.595

Asia WGS AF: 0.390 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.3
DANN	Benign	0.65
PhyloP100		0.51
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs875971; hg19: chr7-65617595;