rs138518275

Variant names:

• chr16-84849391-C-T
• rs138518275
• NM_031476.4:c.366C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-84849391-C-T
• chr16-84849391-C-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Strong BP6 BP7 BS2

The NM_031476.4(CRISPLD2):​c.366C>T​(p.Arg122Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0011 in 1,613,082 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.00098 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0011 (3 hom.)
• Consequence: CRISPLD2 NM_031476.4 synonymous
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -1.15
• Publications: 1 publications found

Genes affected

CRISPLD2 (HGNC:25248): (cysteine rich secretory protein LCCL domain containing 2) Predicted to enable glycosaminoglycan binding activity. Involved in face morphogenesis. Located in transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000285848 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BP6: Variant 16-84849391-C-T is Benign according to our data. Variant chr16-84849391-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3049850.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP7: Synonymous conserved (PhyloP=-1.15 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 3 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031476.4. 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
	CRISPLD2	NM_031476.4	MANE Select	c.366C>T	p.Arg122Arg	synonymous	Exon 4 of 15	NP_113664.1	Q9H0B8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRISPLD2	ENST00000262424.10	TSL:1 MANE Select	c.366C>T	p.Arg122Arg	synonymous	Exon 4 of 15	ENSP00000262424.5	Q9H0B8-1
	CRISPLD2	ENST00000564567.5	TSL:1	c.366C>T	p.Arg122Arg	synonymous	Exon 4 of 13	ENSP00000457655.1	Q9H0B8-2
	CRISPLD2	ENST00000941702.1		c.366C>T	p.Arg122Arg	synonymous	Exon 4 of 15	ENSP00000611761.1

Frequencies

GnomAD3 genomes AF: 0.000985 AC: 150 AN: 152228 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000327

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00141

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00178

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000917 AC: 230 AN: 250814 AF XY: 0.000915

Gnomad AFR exome AF: 0.000185

Gnomad AMR exome AF: 0.000289

Gnomad ASJ exome AF: 0.000199

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00218

Gnomad NFE exome AF: 0.00129

Gnomad OTH exome AF: 0.000981

GnomAD4 exome AF: 0.00111 AC: 1620 AN: 1460736 Hom.: 3 Cov.: 42 AF XY: 0.00115 AC XY: 837 AN XY: 726506

African (AFR) AF: 0.000179 AC: 6 AN: 33466

American (AMR) AF: 0.000291 AC: 13 AN: 44700

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26114

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39668

South Asian (SAS) AF: 0.000406 AC: 35 AN: 86190

European-Finnish (FIN) AF: 0.00257 AC: 137 AN: 53400

Middle Eastern (MID) AF: 0.00141 AC: 8 AN: 5666

European-Non Finnish (NFE) AF: 0.00121 AC: 1349 AN: 1111212

Other (OTH) AF: 0.00118 AC: 71 AN: 60320

GnomAD4 genome AF: 0.000985 AC: 150 AN: 152346 Hom.: 0 Cov.: 33 AF XY: 0.000711 AC XY: 53 AN XY: 74502

African (AFR) AF: 0.000192 AC: 8 AN: 41584

American (AMR) AF: 0.000327 AC: 5 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4832

European-Finnish (FIN) AF: 0.00141 AC: 15 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00178 AC: 121 AN: 68032

Other (OTH) AF: 0.00 AC: 0 AN: 2114

Alfa AF: 0.00120 Hom.: 0

Bravo AF: 0.000756

EpiCase AF: 0.00185

EpiControl AF: 0.00142

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	CRISPLD2-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.8
DANN	Benign	0.67
PhyloP100		-1.2
PromoterAI		0.017	Neutral
Mutation Taster		=97/3	polymorphism

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: rs138518275; hg19: chr16-84882997;