Variant rs72836561 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_145273.4(CD300LG):c.244C>T(p.Arg82Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 1,614,084 control chromosomes in the GnomAD database, including 700 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 0.020 ( 41 hom., cov: 32)

Exomes 𝑓: 0.028 ( 659 hom. )

Consequence

CD300LG
NM_145273.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.282

Variant links:

Genes affected

CD300LG (HGNC:30455): (CD300 molecule like family member g) Members of the CD300 (see MIM 606786)-like (CD300L) family, such as CD300LG, are widely expressed on hematopoietic cells. All CD300L proteins are type I cell surface glycoproteins that contain a single immunoglobulin (Ig) V-like domain (Takatsu et al., 2006 [PubMed 16876123]).[supplied by OMIM, Mar 2008]

CD300LG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.014021635).

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0203 (3089/152240) while in subpopulation NFE AF= 0.0309 (2102/68012). AF 95% confidence interval is 0.0298. There are 41 homozygotes in gnomad4. There are 1472 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 41 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD300LG	NM_145273.4 linkuse as main transcript	c.244C>T	p.Arg82Cys	missense_variant	2/7	ENST00000317310.5	NP_660316.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD300LG	ENST00000317310.5 linkuse as main transcript	c.244C>T	p.Arg82Cys	missense_variant	2/7	1	NM_145273.4	ENSP00000321005	P2	Q6UXG3-1

Frequencies

GnomAD3 genomes

AF:

0.0203

AC:

3092

AN:

152122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00534

Gnomad AMI

AF:

0.00879

Gnomad AMR

AF:

0.0167

Gnomad ASJ

AF:

0.0104

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0224

Gnomad FIN

AF:

0.0299

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0309

Gnomad OTH

AF:

0.0191

GnomAD3 exomes

AF:

0.0219

AC:

5498

AN:

251414

Hom.:

101

AF XY:

0.0223

AC XY:

3035

AN XY:

135890

show subpopulations

Gnomad AFR exome

AF:

0.00523

Gnomad AMR exome

AF:

0.00942

Gnomad ASJ exome

AF:

0.0101

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0242

Gnomad FIN exome

AF:

0.0287

Gnomad NFE exome

AF:

0.0308

Gnomad OTH exome

AF:

0.0194

GnomAD4 exome

AF:

0.0277

AC:

40424

AN:

1461844

Hom.:

659

Cov.:

AF XY:

0.0274

AC XY:

19921

AN XY:

727218

show subpopulations

Gnomad4 AFR exome

AF:

0.00451

Gnomad4 AMR exome

AF:

0.0101

Gnomad4 ASJ exome

AF:

0.00983

Gnomad4 EAS exome

AF:

0.000202

Gnomad4 SAS exome

AF:

0.0235

Gnomad4 FIN exome

AF:

0.0314

Gnomad4 NFE exome

AF:

0.0310

Gnomad4 OTH exome

AF:

0.0214

GnomAD4 genome

AF:

0.0203

AC:

3089

AN:

152240

Hom.:

Cov.:

AF XY:

0.0198

AC XY:

1472

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.00532

Gnomad4 AMR

AF:

0.0167

Gnomad4 ASJ

AF:

0.0104

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0222

Gnomad4 FIN

AF:

0.0299

Gnomad4 NFE

AF:

0.0309

Gnomad4 OTH

AF:

0.0185

Alfa

AF:

0.0267

Hom.:

109

Bravo

AF:

0.0179

TwinsUK

AF:

0.0305

AC:

113

ALSPAC

AF:

0.0283

AC:

109

ESP6500AA

AF:

0.00658

AC:

ESP6500EA

AF:

0.0303

AC:

261

ExAC

AF:

0.0225

AC:

2733

Asia WGS

AF:

0.0110

AC:

AN:

3478

EpiCase

AF:

0.0248

EpiControl

AF:

0.0236

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.30

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.39

.;.;.;.;.;T

Eigen

Benign

-0.085

Eigen_PC

Benign

-0.35

FATHMM_MKL

Benign

0.053

LIST_S2

Benign

0.66

T;T;T;T;T;T

MetaRNN

Benign

0.014

T;T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.8

M;M;.;M;M;M

MutationTaster

Benign

1.0

N;N;N;N;N;N

PrimateAI

Benign

0.18

PROVEAN

Pathogenic

-6.2

D;D;.;D;.;D

REVEL

Benign

0.049

Sift

Pathogenic

0.0

D;D;.;D;.;D

Sift4G

Uncertain

0.0020

D;D;D;D;D;D

Polyphen

1.0

.;.;.;D;D;D

Vest4

0.066

MPC

0.055

ClinPred

0.065

GERP RS

1.1

Varity_R

0.32

gMVP

0.34

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over