6-49846584-G-C

Variant names:

• chr6-49846584-G-C
• NM_001131.3:c.371C>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001131.3(CRISP1):​c.371C>G​(p.Thr124Arg) variant causes a missense 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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CRISP1 NM_001131.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.645

Genes affected

CRISP1 (HGNC:304): (cysteine rich secretory protein 1) Fertilization consists of a sequence of specific cell-cell interactions culminating in the fusion of the sperm and egg plasma membranes. Recognition, binding, and fusion occur through the interaction of complementary molecules that are localized to specific domains of the sperm and egg plasma membranes. In the sperm, the postacrosomal region or equatorial segment is involved in sperm-egg plasma membrane fusion. The protein encoded by this gene is a member of the cysteine-rich secretory protein (CRISP) family. It is expressed in the epididymis, is secreted into the epididymal lumen, and binds to the postacrosomal region of the sperm head, where it plays a role in sperm-egg fusion. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.03868246).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRISP1	NM_001131.3	c.371C>G	p.Thr124Arg	missense_variant	Exon 5 of 8	ENST00000335847.9	NP_001122.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRISP1	ENST00000335847.9	c.371C>G	p.Thr124Arg	missense_variant	Exon 5 of 8	1	NM_001131.3	ENSP00000338276.4
CRISP1	ENST00000505118.1	c.371C>G	p.Thr124Arg	missense_variant	Exon 5 of 8	1		ENSP00000427589.1
CRISP1	ENST00000507853.5	c.371C>G	p.Thr124Arg	missense_variant	Exon 5 of 7	1		ENSP00000425020.1
CRISP1	ENST00000329411.9	c.371C>G	p.Thr124Arg	missense_variant	Exon 4 of 6	5		ENSP00000331317.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Feb 17, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.371C>G (p.T124R) alteration is located in exon 5 (coding exon 4) of the CRISP1 gene. This alteration results from a C to G substitution at nucleotide position 371, causing the threonine (T) at amino acid position 124 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.078
BayesDel_addAF	Benign	-0.37	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.3
DANN	Benign	0.45
DEOGEN2	Benign	0.027	.;T;.;T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.020	N
LIST_S2	Benign	0.30	.;.;T;T
M_CAP	Benign	0.0025	T
MetaRNN	Benign	0.039	T;T;T;T
MetaSVM	Benign	-0.91	T
MutationAssessor	Benign	-0.17	N;N;N;N
PrimateAI	Benign	0.31	T
PROVEAN	Benign	1.6	N;N;N;N
REVEL	Benign	0.023
Sift	Benign	0.38	T;T;T;T
Sift4G	Benign	0.20	T;T;T;T
Polyphen		0.0	B;B;B;B
Vest4		0.092
MutPred		0.41		Loss of ubiquitination at K127 (P = 0.0574);Loss of ubiquitination at K127 (P = 0.0574);Loss of ubiquitination at K127 (P = 0.0574);Loss of ubiquitination at K127 (P = 0.0574);
MVP		0.18
MPC		0.015
ClinPred		0.044	T
GERP RS		3.0
Varity_R		0.038
gMVP		0.21

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-49814297;