rs10957748

Positions:

• chr8-75027166-C-T

Variant summary

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

The NM_031461.6(CRISPLD1):​c.1320+1545C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,836 control chromosomes in the GnomAD database, including 10,340 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 0.35 (10340 hom., cov: 31)
• Consequence: CRISPLD1 NM_031461.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRISPLD1	NM_031461.6	c.1320+1545C>T		intron_variant		ENST00000262207.9
LOC124901964	XR_007060966.1	n.298-231G>A		intron_variant, non_coding_transcript_variant
CRISPLD1	NM_001286777.2	c.762+1545C>T		intron_variant
CRISPLD1	NM_001286778.2	c.756+1545C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRISPLD1	ENST00000262207.9	c.1320+1545C>T		intron_variant		1	NM_031461.6	P1
	ENST00000520778.1	n.83-231G>A		intron_variant, non_coding_transcript_variant		3
CRISPLD1	ENST00000517786.1	c.762+1545C>T		intron_variant		2
CRISPLD1	ENST00000523524.5	c.756+1545C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53362 AN: 151718 Hom.: 10311 Cov.: 31

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.352 AC: 53441 AN: 151836 Hom.: 10340 Cov.: 31 AF XY: 0.351 AC XY: 26042 AN XY: 74208

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.327

Alfa AF: 0.292 Hom.: 8901

Bravo AF: 0.350

Asia WGS AF: 0.253 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.58

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: rs10957748; hg19: chr8-75939401;