8-74990527-A-G

Position:

• chr8-74990527-A-G

Variant summary

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

The NM_031461.6(CRISPLD1):​c.258+4282A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,628 control chromosomes in the GnomAD database, including 17,248 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 0.44 (17248 hom., cov: 31)
• Consequence: CRISPLD1 NM_031461.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94

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]

CRISPLD1 (HGNC:):

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 = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRISPLD1	NM_031461.6	c.258+4282A>G		intron_variant		ENST00000262207.9	NP_113649.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRISPLD1	ENST00000262207.9	c.258+4282A>G		intron_variant		1	NM_031461.6	ENSP00000262207.4
CRISPLD1	ENST00000520277.1	c.258+4282A>G		intron_variant		5		ENSP00000430504.1
CRISPLD1	ENST00000519798.1	n.511+4410A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66264 AN: 151510 Hom.: 17198 Cov.: 31

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.438 AC: 66374 AN: 151628 Hom.: 17248 Cov.: 31 AF XY: 0.435 AC XY: 32202 AN XY: 74060

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.406

Alfa AF: 0.280 Hom.: 933

Bravo AF: 0.444

Asia WGS AF: 0.329 AC: 1145 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	0.0080
DANN	Benign	0.28

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: rs7841231; hg19: chr8-75902762;