8-75011592-G-C

Variant summary

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

The NM_031461.6(CRISPLD1):c.259-841G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 151,914 control chromosomes in the GnomAD database, including 39,482 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 0.71 (39482 hom., cov: 31)
• Consequence: CRISPLD1 NM_031461.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

Genes affected

CRISPLD1 (HGNC:18206): (cysteine rich secretory protein LCCL domain containing 1) Involved in face morphogenesis. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRISPLD1	NM_031461.6	c.259-841G>C		intron_variant		ENST00000262207.9
CRISPLD1	NM_001286777.2	c.-184-841G>C		intron_variant
CRISPLD1	NM_001286778.2	c.-306-841G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRISPLD1	ENST00000262207.9	c.259-841G>C		intron_variant		1	NM_031461.6	P1

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107317 AN: 151796 Hom.: 39427 Cov.: 31

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.707 AC: 107435 AN: 151914 Hom.: 39482 Cov.: 31 AF XY: 0.706 AC XY: 52405 AN XY: 74238

Gnomad4 AFR AF: 0.922

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.695

Alfa AF: 0.663 Hom.: 4048

Bravo AF: 0.711

Asia WGS AF: 0.677 AC: 2356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.066
Dann	Benign	0.50

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: rs1455796; hg19: chr8-75923827;