6-49690557-C-T

Variant names:

• chr6-49690557-C-T
• rs360563
• XM_011514843.4:c.709+5279G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_926302.4(CRISP2):​n.928+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 XR_926302.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.699 AC: 28965 AN: 41436

American (AMR) AF: 0.653 AC: 9967 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1482 AN: 3464

East Asian (EAS) AF: 0.803 AC: 4161 AN: 5180

South Asian (SAS) AF: 0.640 AC: 3089 AN: 4824

European-Finnish (FIN) AF: 0.564 AC: 5935 AN: 10520

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34913 AN: 67804

Other (OTH) AF: 0.569 AC: 1198 AN: 2106

Alfa AF: 0.551 Hom.: 2908

Bravo AF: 0.608

Asia WGS AF: 0.742 AC: 2571 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.60
DANN	Benign	0.40
PhyloP100		-0.54

Splicing

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

Other links and lift over

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