8-75000832-T-C

Variant names:

• chr8-75000832-T-C
• rs1455809
• NM_031461.6:c.259-11601T>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.259-11601T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,690 control chromosomes in the GnomAD database, including 16,716 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 0.43 (16716 hom., cov: 30)
• Consequence: CRISPLD1 NM_031461.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRISPLD1	NM_031461.6	c.259-11601T>C		intron_variant	Intron 2 of 14	ENST00000262207.9	NP_113649.1
CRISPLD1	NM_001286777.2	c.-185+423T>C		intron_variant	Intron 1 of 12		NP_001273706.1
CRISPLD1	NM_001286778.2	c.-307+423T>C		intron_variant	Intron 1 of 13		NP_001273707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRISPLD1	ENST00000262207.9	c.259-11601T>C		intron_variant	Intron 2 of 14	1	NM_031461.6	ENSP00000262207.4

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64801 AN: 151572 Hom.: 16664 Cov.: 30

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.428 AC: 64911 AN: 151690 Hom.: 16716 Cov.: 30 AF XY: 0.425 AC XY: 31491 AN XY: 74086

African (AFR) AF: 0.737 AC: 30424 AN: 41306

American (AMR) AF: 0.287 AC: 4368 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 899 AN: 3464

East Asian (EAS) AF: 0.298 AC: 1534 AN: 5146

South Asian (SAS) AF: 0.282 AC: 1357 AN: 4804

European-Finnish (FIN) AF: 0.374 AC: 3927 AN: 10488

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21194 AN: 67944

Other (OTH) AF: 0.401 AC: 840 AN: 2096

Alfa AF: 0.361 Hom.: 4356

Bravo AF: 0.435

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.59
DANN	Benign	0.56
PhyloP100		-0.51
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: rs1455809; hg19: chr8-75913067;