Variant 2-46758587-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_144949.3(SOCS5):c.57C>T(p.Phe19Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00283 in 1,611,998 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0021 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0029 ( 16 hom. )

Consequence

SOCS5
NM_144949.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.578

Variant links:

Genes affected

SOCS5 (HGNC:16852): (suppressor of cytokine signaling 5) The protein encoded by this gene contains a SH2 domain and a SOCS BOX domain. The protein thus belongs to the suppressor of cytokine signaling (SOCS) family, also known as STAT-induced STAT inhibitor (SSI) protein family. SOCS family members are known to be cytokine-inducible negative regulators of cytokine signaling. The specific function of this protein has not yet been determined. Two alternatively spliced transcript variants encoding an identical protein have been reported. [provided by RefSeq, Jul 2008]

SOCS5 links:

LINC01118 (HGNC:):

LINC01118 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP6

Variant 2-46758587-C-T is Benign according to our data. Variant chr2-46758587-C-T is described in ClinVar as [Benign]. Clinvar id is 720047.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.578 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 16 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOCS5	NM_144949.3 linkuse as main transcript	c.57C>T	p.Phe19Phe	synonymous_variant	2/2	ENST00000394861.3	NP_659198.1	O75159
SOCS5	NM_014011.5 linkuse as main transcript	c.57C>T	p.Phe19Phe	synonymous_variant	2/2		NP_054730.1	O75159

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SOCS5	ENST00000394861.3 linkuse as main transcript	c.57C>T	p.Phe19Phe	synonymous_variant	2/2	1	NM_144949.3	ENSP00000378330.2	O75159
SOCS5	ENST00000306503.5 linkuse as main transcript	c.57C>T	p.Phe19Phe	synonymous_variant	2/2	1		ENSP00000305133.5	O75159
LINC01118	ENST00000650611.1 linkuse as main transcript	n.173-38732C>T		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.00215

AC:

327

AN:

152142

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000338

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00308

Gnomad ASJ

AF:

0.00432

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00350

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00201

AC:

500

AN:

249252

Hom.:

AF XY:

0.00206

AC XY:

277

AN XY:

134644

show subpopulations

Gnomad AFR exome

AF:

0.000308

Gnomad AMR exome

AF:

0.00234

Gnomad ASJ exome

AF:

0.00571

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000733

Gnomad FIN exome

AF:

0.000232

Gnomad NFE exome

AF:

0.00281

Gnomad OTH exome

AF:

0.00230

GnomAD4 exome

AF:

0.00290

AC:

4228

AN:

1459738

Hom.:

Cov.:

AF XY:

0.00284

AC XY:

2059

AN XY:

726134

show subpopulations

Gnomad4 AFR exome

AF:

0.000480

Gnomad4 AMR exome

AF:

0.00237

Gnomad4 ASJ exome

AF:

0.00529

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000595

Gnomad4 FIN exome

AF:

0.000187

Gnomad4 NFE exome

AF:

0.00336

Gnomad4 OTH exome

AF:

0.00265

GnomAD4 genome

AF:

0.00215

AC:

327

AN:

152260

Hom.:

Cov.:

AF XY:

0.00191

AC XY:

142

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.000337

Gnomad4 AMR

AF:

0.00307

Gnomad4 ASJ

AF:

0.00432

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000622

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.00350

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00320

Hom.:

Bravo

AF:

0.00220

EpiCase

AF:

0.00311

EpiControl

AF:

0.00279

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

DANN

Benign

0.73

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over