Variant 19-39657944-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001190441.3(LGALS16):c.77T>C(p.Leu26Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0129 in 1,613,958 control chromosomes in the GnomAD database, including 1,931 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.063 ( 1001 hom., cov: 32)

Exomes 𝑓: 0.0076 ( 930 hom. )

Consequence

LGALS16
NM_001190441.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.990

Variant links:

Genes affected

LGALS16 (HGNC:40039): (galectin 16) Enables lactose binding activity. Involved in positive regulation of T cell apoptotic process. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LGALS16 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=0.01038757).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LGALS16	NM_001190441.3 linkuse as main transcript	c.77T>C	p.Leu26Pro	missense_variant	2/4	ENST00000392051.4	NP_001177370.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LGALS16	ENST00000392051.4 linkuse as main transcript	c.77T>C	p.Leu26Pro	missense_variant	2/4	1	NM_001190441.3	ENSP00000375904	P1
LGALS16	ENST00000594480.1 linkuse as main transcript	c.132T>C	p.Thr44=	synonymous_variant, NMD_transcript_variant	2/4	3		ENSP00000471564

Frequencies

GnomAD3 genomes

AF:

0.0633

AC:

9632

AN:

152190

Hom.:

998

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0220

Gnomad ASJ

AF:

0.0516

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00103

Gnomad OTH

AF:

0.0463

GnomAD3 exomes

AF:

0.0185

AC:

4652

AN:

251258

Hom.:

424

AF XY:

0.0140

AC XY:

1902

AN XY:

135786

show subpopulations

Gnomad AFR exome

AF:

0.222

Gnomad AMR exome

AF:

0.00983

Gnomad ASJ exome

AF:

0.0504

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000327

Gnomad FIN exome

AF:

0.0000464

Gnomad NFE exome

AF:

0.00108

Gnomad OTH exome

AF:

0.0103

GnomAD4 exome

AF:

0.00760

AC:

11105

AN:

1461650

Hom.:

930

Cov.:

AF XY:

0.00675

AC XY:

4909

AN XY:

727138

show subpopulations

Gnomad4 AFR exome

AF:

0.226

Gnomad4 AMR exome

AF:

0.0108

Gnomad4 ASJ exome

AF:

0.0492

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000394

Gnomad4 FIN exome

AF:

0.0000188

Gnomad4 NFE exome

AF:

0.000554

Gnomad4 OTH exome

AF:

0.0177

GnomAD4 genome

AF:

0.0634

AC:

9661

AN:

152308

Hom.:

1001

Cov.:

AF XY:

0.0609

AC XY:

4539

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.216

Gnomad4 AMR

AF:

0.0221

Gnomad4 ASJ

AF:

0.0516

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000827

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00103

Gnomad4 OTH

AF:

0.0458

Alfa

AF:

0.0117

Hom.:

170

Bravo

AF:

0.0718

TwinsUK

AF:

0.00108

AC:

ALSPAC

AF:

0.000778

AC:

ExAC

AF:

0.0218

AC:

2650

Asia WGS

AF:

0.0150

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.73

CADD

Benign

0.12

DANN

Benign

0.039

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.00014

MetaRNN

Benign

0.010

MetaSVM

Benign

-0.92

MutationTaster

Benign

1.0

PrimateAI

Benign

0.33

PROVEAN

Benign

4.1

REVEL

Benign

0.058

Sift

Benign

1.0

Sift4G

Benign

0.68

Vest4

0.033

MPC

0.037

ClinPred

0.00011

GERP RS

0.065

gMVP

0.52

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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