6-49690557-C-T

Position:

• chr6-49690557-C-T

Variant summary

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

The XM_011514843.4(CRISP2):​c.709+5279G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,794 control chromosomes in the GnomAD database, including 27,560 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 (27560 hom., cov: 32)
• Consequence: CRISP2 XM_011514843.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

Genes affected

CRISP2 (HGNC:12024): (cysteine rich secretory protein 2) Predicted to be involved in cell-cell adhesion. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRISP2	XM_011514843.4	c.709+5279G>A		intron_variant			XP_011513145.1
		n.49690557C>T		intergenic_region
CRISP2	XR_926302.4	n.928+5279G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90212 AN: 151674 Hom.: 27515 Cov.: 32

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.565

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.595 AC: 90315 AN: 151794 Hom.: 27560 Cov.: 32 AF XY: 0.600 AC XY: 44499 AN XY: 74172

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.569

Alfa AF: 0.545 Hom.: 2726

Bravo AF: 0.608

Asia WGS AF: 0.742 AC: 2571 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.60
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs360563; hg19: chr6-49658270; COSMIC: COSV59255966;