7-66130821-C-T

Variant names:

• chr7-66130821-C-T
• rs1787778670
• NM_014478.5:c.123C>T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_014478.5(CRCP):​c.123C>T​(p.Asn41Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: CRCP NM_014478.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.27
• Publications: 0 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]

ENSG00000249319 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.069).
• BP7: Synonymous conserved (PhyloP=2.27 with no splicing effect.

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.123C>T	p.Asn41Asn	synonymous	Exon 3 of 6	NP_055293.1	O75575-1
	CRCP	NM_001142414.1		c.123+3081C>T		intron	N/A	NP_001135886.1	O75575-3
	CRCP	NM_001040647.2		c.45+3081C>T		intron	N/A	NP_001035737.1	O75575-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRCP	ENST00000395326.8	TSL:1 MANE Select	c.123C>T	p.Asn41Asn	synonymous	Exon 3 of 6	ENSP00000378736.3	O75575-1
	ENSG00000249319	ENST00000450043.2	TSL:5	c.678C>T	p.Asn226Asn	synonymous	Exon 9 of 12	ENSP00000396527.2	H7C0S8
	CRCP	ENST00000338592.5	TSL:1	c.45+3081C>T		intron	N/A	ENSP00000340044.5	O75575-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 24

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	8.4
DANN	Benign	0.84
PhyloP100		2.3

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: rs1787778670; hg19: chr7-65595808;