Variant 12-7368939-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_174941.6(CD163L1):c.4066T>C(p.Ser1356Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00296 in 1,613,598 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0021 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0030 ( 5 hom. )

Consequence

CD163L1
NM_174941.6 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0420

Variant links:

Genes affected

CD163L1 (HGNC:30375): (CD163 molecule like 1) This gene encodes a member of the scavenger receptor cysteine-rich (SRCR) superfamily. Members of this family are secreted or membrane-anchored proteins mainly found in cells associated with the immune system. The SRCR family is defined by a 100-110 amino acid SRCR domain, which may mediate protein-protein interaction and ligand binding. The encoded protein contains twelve SRCR domains, a transmembrane region and a cytoplasmic domain. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2014]

CD163L1 links:

CD163L1 (HGNC:):

CD163L1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.006833434).

BP6

Variant 12-7368939-A-G is Benign according to our data. Variant chr12-7368939-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3024838.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD163L1	NM_174941.6 linkuse as main transcript	c.4066T>C	p.Ser1356Pro	missense_variant	16/20	ENST00000313599.8	NP_777601.3	Q9NR16-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD163L1	ENST00000313599.8 linkuse as main transcript	c.4066T>C	p.Ser1356Pro	missense_variant	16/20	1	NM_174941.6	ENSP00000315945.3		Q9NR16-1

Frequencies

GnomAD3 genomes

AF:

0.00209

AC:

318

AN:

152010

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000822

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00209

Gnomad ASJ

AF:

0.00779

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000624

Gnomad FIN

AF:

0.000567

Gnomad MID

AF:

0.0159

Gnomad NFE

AF:

0.00304

Gnomad OTH

AF:

0.00192

GnomAD3 exomes

AF:

0.00245

AC:

616

AN:

251262

Hom.:

AF XY:

0.00264

AC XY:

358

AN XY:

135802

show subpopulations

Gnomad AFR exome

AF:

0.000492

Gnomad AMR exome

AF:

0.00257

Gnomad ASJ exome

AF:

0.00725

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000392

Gnomad FIN exome

AF:

0.000650

Gnomad NFE exome

AF:

0.00347

Gnomad OTH exome

AF:

0.00424

GnomAD4 exome

AF:

0.00305

AC:

4455

AN:

1461470

Hom.:

Cov.:

AF XY:

0.00314

AC XY:

2280

AN XY:

727024

show subpopulations

Gnomad4 AFR exome

AF:

0.000598

Gnomad4 AMR exome

AF:

0.00268

Gnomad4 ASJ exome

AF:

0.00842

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000719

Gnomad4 FIN exome

AF:

0.000920

Gnomad4 NFE exome

AF:

0.00341

Gnomad4 OTH exome

AF:

0.00296

GnomAD4 genome

AF:

0.00208

AC:

317

AN:

152128

Hom.:

Cov.:

AF XY:

0.00198

AC XY:

147

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.000819

Gnomad4 AMR

AF:

0.00209

Gnomad4 ASJ

AF:

0.00779

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000624

Gnomad4 FIN

AF:

0.000567

Gnomad4 NFE

AF:

0.00304

Gnomad4 OTH

AF:

0.00190

Alfa

AF:

0.00325

Hom.:

Bravo

AF:

0.00207

TwinsUK

AF:

0.00270

AC:

ALSPAC

AF:

0.00441

AC:

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.00291

AC:

ExAC

AF:

0.00223

AC:

271

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00278

EpiControl

AF:

0.00290

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2024

CD163L1: BP4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.086

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.55

CADD

Benign

DANN

Benign

0.26

DEOGEN2

Benign

0.0037

T;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.0069

LIST_S2

Benign

0.30

T;T

M_CAP

Benign

0.0021

MetaRNN

Benign

0.0068

T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

0.0

N;.

PrimateAI

Benign

0.36

PROVEAN

Benign

-0.20

N;N

REVEL

Benign

0.081

Sift

Benign

0.14

T;T

Sift4G

Benign

0.37

T;T

Polyphen

0.96

D;.

Vest4

0.28

MVP

0.23

MPC

0.40

ClinPred

0.0050

GERP RS

-0.84

Varity_R

0.15

gMVP

0.75

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over