8-75011592-G-C

Variant names:

• chr8-75011592-G-C
• rs1455796
• NM_031461.6:c.259-841G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031461.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRISPLD1	NM_031461.6	MANE Select	c.259-841G>C		intron	N/A	NP_113649.1	Q9H336-1
	CRISPLD1	NM_001286777.2		c.-184-841G>C		intron	N/A	NP_001273706.1	Q9H336-2
	CRISPLD1	NM_001286778.2		c.-306-841G>C		intron	N/A	NP_001273707.1	B7Z8V9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRISPLD1	ENST00000262207.9	TSL:1 MANE Select	c.259-841G>C		intron	N/A	ENSP00000262207.4	Q9H336-1
	CRISPLD1	ENST00000959492.1		c.259-841G>C		intron	N/A	ENSP00000629551.1
	CRISPLD1	ENST00000916000.1		c.259-841G>C		intron	N/A	ENSP00000586059.1

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

African (AFR) AF: 0.922 AC: 38271 AN: 41488

American (AMR) AF: 0.614 AC: 9348 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2050 AN: 3472

East Asian (EAS) AF: 0.635 AC: 3272 AN: 5154

South Asian (SAS) AF: 0.584 AC: 2810 AN: 4808

European-Finnish (FIN) AF: 0.738 AC: 7789 AN: 10554

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41658 AN: 67902

Other (OTH) AF: 0.695 AC: 1467 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.066
DANN	Benign	0.50
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1455796; hg19: chr8-75923827;