Variant 11-193722-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7

The NM_145651.3(SCGB1C1):c.66A>G(p.Thr22Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.027 ( 1 hom., cov: 29)

Exomes 𝑓: 0.0029 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

SCGB1C1
NM_145651.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.04

Variant links:

Genes affected

SCGB1C1 (HGNC:18394): (secretoglobin family 1C member 1) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

SCGB1C1 links:

BET1L (HGNC:19348): (Bet1 golgi vesicular membrane trafficking protein like) Enables SNAP receptor activity. Involved in regulation of retrograde vesicle-mediated transport, Golgi to ER and retrograde transport, endosome to Golgi. Located in Golgi apparatus and endosome. Implicated in uterine fibroid. Biomarker of endometrial adenocarcinoma. [provided by Alliance of Genome Resources, Apr 2022]

BET1L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 11-193722-A-G is Benign according to our data. Variant chr11-193722-A-G is described in ClinVar as [Benign]. Clinvar id is 768405.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.04 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCGB1C1	NM_145651.3 linkuse as main transcript	c.66A>G	p.Thr22Thr	synonymous_variant	2/3	ENST00000342878.3	NP_663626.2	Q8TD33
SCGB1C1	XM_005252804.4 linkuse as main transcript	c.195A>G	p.Thr65Thr	synonymous_variant	3/4		XP_005252861.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCGB1C1	ENST00000342878.3 linkuse as main transcript	c.66A>G	p.Thr22Thr	synonymous_variant	2/3	1	NM_145651.3	ENSP00000344545.2		Q8TD33
BET1L	ENST00000410108.5 linkuse as main transcript	c.168+11889T>C		intron_variant		3		ENSP00000386558.1		B8ZZS0

Frequencies

GnomAD3 genomes

AF:

0.0266

AC:

3220

AN:

120966

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0275

Gnomad AMI

AF:

0.0343

Gnomad AMR

AF:

0.0518

Gnomad ASJ

AF:

0.0111

Gnomad EAS

AF:

0.150

Gnomad SAS

AF:

0.0780

Gnomad FIN

AF:

0.0117

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0142

Gnomad OTH

AF:

0.0244

GnomAD3 exomes

AF:

0.193

AC:

43760

AN:

227120

Hom.:

AF XY:

0.191

AC XY:

23618

AN XY:

123396

show subpopulations

Gnomad AFR exome

AF:

0.187

Gnomad AMR exome

AF:

0.275

Gnomad ASJ exome

AF:

0.133

Gnomad EAS exome

AF:

0.405

Gnomad SAS exome

AF:

0.299

Gnomad FIN exome

AF:

0.106

Gnomad NFE exome

AF:

0.128

Gnomad OTH exome

AF:

0.177

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00289

AC:

4044

AN:

1398092

Hom.:

Cov.:

AF XY:

0.00294

AC XY:

2036

AN XY:

693086

show subpopulations

Gnomad4 AFR exome

AF:

0.00302

Gnomad4 AMR exome

AF:

0.00548

Gnomad4 ASJ exome

AF:

0.00214

Gnomad4 EAS exome

AF:

0.0683

Gnomad4 SAS exome

AF:

0.00198

Gnomad4 FIN exome

AF:

0.00298

Gnomad4 NFE exome

AF:

0.00112

Gnomad4 OTH exome

AF:

0.00380

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0266

AC:

3224

AN:

121066

Hom.:

Cov.:

AF XY:

0.0290

AC XY:

1712

AN XY:

58936

show subpopulations

Gnomad4 AFR

AF:

0.0274

Gnomad4 AMR

AF:

0.0520

Gnomad4 ASJ

AF:

0.0111

Gnomad4 EAS

AF:

0.150

Gnomad4 SAS

AF:

0.0781

Gnomad4 FIN

AF:

0.0117

Gnomad4 NFE

AF:

0.0142

Gnomad4 OTH

AF:

0.0241

Alfa

AF:

0.104

Hom.:

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.2

DANN

Benign

0.46

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