Variant 20-23036182-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001052.4(SSTR4):c.699C>T(p.Leu233=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00611 in 1,611,514 control chromosomes in the GnomAD database, including 65 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0087 ( 6 hom., cov: 33)

Exomes 𝑓: 0.0058 ( 59 hom. )

Consequence

SSTR4
NM_001052.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.48

Variant links:

Genes affected

SSTR4 (HGNC:11333): (somatostatin receptor 4) Somatostatin acts at many sites to inhibit the release of many hormones and other secretory proteins. The biologic effects of somatostatin are probably mediated by a family of G protein-coupled receptors that are expressed in a tissue-specific manner. SSTR4 is a member of the superfamily of receptors having seven transmembrane segments and is expressed in highest levels in fetal and adult brain and lung. [provided by RefSeq, Jul 2008]

SSTR4 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 20-23036182-C-T is Benign according to our data. Variant chr20-23036182-C-T is described in ClinVar as [Benign]. Clinvar id is 782169.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.48 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00584 (8527/1459188) while in subpopulation MID AF= 0.0512 (295/5762). AF 95% confidence interval is 0.0464. There are 59 homozygotes in gnomad4_exome. There are 4420 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SSTR4	NM_001052.4 linkuse as main transcript	c.699C>T	p.Leu233=	synonymous_variant	1/1	ENST00000255008.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SSTR4	ENST00000255008.5 linkuse as main transcript	c.699C>T	p.Leu233=	synonymous_variant	1/1		NM_001052.4	P1
	ENST00000440921.6 linkuse as main transcript	n.827-2041C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00872

AC:

1327

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0139

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0126

Gnomad ASJ

AF:

0.0112

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00600

Gnomad FIN

AF:

0.00122

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.00607

Gnomad OTH

AF:

0.0196

GnomAD3 exomes

AF:

0.00726

AC:

1791

AN:

246582

Hom.:

AF XY:

0.00750

AC XY:

1004

AN XY:

133918

show subpopulations

Gnomad AFR exome

AF:

0.0126

Gnomad AMR exome

AF:

0.00853

Gnomad ASJ exome

AF:

0.0154

Gnomad EAS exome

AF:

0.000112

Gnomad SAS exome

AF:

0.00890

Gnomad FIN exome

AF:

0.00109

Gnomad NFE exome

AF:

0.00692

Gnomad OTH exome

AF:

0.0132

GnomAD4 exome

AF:

0.00584

AC:

8527

AN:

1459188

Hom.:

Cov.:

AF XY:

0.00609

AC XY:

4420

AN XY:

725996

show subpopulations

Gnomad4 AFR exome

AF:

0.0146

Gnomad4 AMR exome

AF:

0.00862

Gnomad4 ASJ exome

AF:

0.0142

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00759

Gnomad4 FIN exome

AF:

0.00103

Gnomad4 NFE exome

AF:

0.00515

Gnomad4 OTH exome

AF:

0.00917

GnomAD4 genome

AF:

0.00869

AC:

1324

AN:

152326

Hom.:

Cov.:

AF XY:

0.00861

AC XY:

641

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.0139

Gnomad4 AMR

AF:

0.0125

Gnomad4 ASJ

AF:

0.0112

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00600

Gnomad4 FIN

AF:

0.00122

Gnomad4 NFE

AF:

0.00607

Gnomad4 OTH

AF:

0.0189

Alfa

AF:

0.00647

Hom.:

Bravo

AF:

0.00948

Asia WGS

AF:

0.00577

AC:

AN:

3478

EpiCase

AF:

0.0100

EpiControl

AF:

0.00842

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 15, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

3.8

DANN

Benign

0.93

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