chr1-152515676-G-A

Position:

• chr1-152515676-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_019060.3(CRCT1):​c.293G>A​(p.Gly98Asp) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CRCT1 NM_019060.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.32

Genes affected

CRCT1 (HGNC:29875): (cysteine rich C-terminal 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRCT1	NM_019060.3	c.293G>A	p.Gly98Asp	missense_variant	2/2	ENST00000368790.4
CRCT1	XM_011509656.3	c.293G>A	p.Gly98Asp	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRCT1	ENST00000368790.4	c.293G>A	p.Gly98Asp	missense_variant	2/2	1	NM_019060.3	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1368906 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 671840

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.042	T
BayesDel_noAF	Benign	-0.30
CADD	Benign	21
DANN	Benign	0.80
DEOGEN2	Benign	0.10	T
Eigen	Uncertain	0.28
Eigen_PC	Benign	0.15
FATHMM_MKL	Benign	0.37	N
LIST_S2	Benign	0.32	T
M_CAP	Uncertain	0.093	D
MetaRNN	Uncertain	0.46	T
MetaSVM	Benign	-0.85	T
MutationTaster	Benign	1.0	N
PROVEAN	Pathogenic	-7.0	D
REVEL	Benign	0.19
Sift4G	Uncertain	0.0070	D
Polyphen		1.0	D
Vest4		0.41
MutPred		0.15		Loss of MoRF binding (P = 0.0528);
MVP		0.58
MPC		0.41
ClinPred		0.94	D
GERP RS		3.8
Varity_R		0.41
gMVP		0.034

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: rs1388893848; hg19: chr1-152488152;