11-193112-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_145651.3(SCGB1C1):c.13C>T(p.Arg5Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.055 (12 hom., cov: 16)
  • Exomes 𝑓: 0.026 (1667 hom.)
  • Failed GnomAD Quality Control
• Consequence: SCGB1C1 NM_145651.3 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.43

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]

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]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0033165812).
• BP6: Variant 11-193112-C-T is Benign according to our data. Variant chr11-193112-C-T is described in ClinVar as [Benign]. Clinvar id is 768404.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCGB1C1	NM_145651.3	c.13C>T	p.Arg5Cys	missense_variant	1/3	ENST00000342878.3
SCGB1C1	XM_005252804.4	c.142C>T	p.Arg48Cys	missense_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCGB1C1	ENST00000342878.3	c.13C>T	p.Arg5Cys	missense_variant	1/3	1	NM_145651.3	P1
BET1L	ENST00000410108.5	c.168+12499G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 4874 AN: 89136 Hom.: 12 Cov.: 16 FAILED QC

Gnomad AFR AF: 0.0212

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0408

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0386

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.0374

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.0608

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0260 AC: 29572 AN: 1136558 Hom.: 1667 Cov.: 30 AF XY: 0.0280 AC XY: 15709 AN XY: 561736

Gnomad4 AFR exome AF: 0.0122

Gnomad4 AMR exome AF: 0.0194

Gnomad4 ASJ exome AF: 0.111

Gnomad4 EAS exome AF: 0.0287

Gnomad4 SAS exome AF: 0.0291

Gnomad4 FIN exome AF: 0.0511

Gnomad4 NFE exome AF: 0.0232

Gnomad4 OTH exome AF: 0.0376

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0546 AC: 4874 AN: 89240 Hom.: 12 Cov.: 16 AF XY: 0.0508 AC XY: 2198 AN XY: 43296

Gnomad4 AFR AF: 0.0214

Gnomad4 AMR AF: 0.0406

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0379

Gnomad4 SAS AF: 0.0457

Gnomad4 FIN AF: 0.0374

Gnomad4 NFE AF: 0.0845

Gnomad4 OTH AF: 0.0609

Alfa AF: 0.250 Hom.: 101

ESP6500AA AF: 0.177 AC: 758

ESP6500EA AF: 0.322 AC: 2740

ExAC AF: 0.302 AC: 36557

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Aug 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.41	T
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.4
Dann	Benign	0.90
DEOGEN2	Benign	0.00097	T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.0045	N
LIST_S2	Benign	0.54	T
MetaRNN	Benign	0.0033	T
MetaSVM	Benign	-0.94	T
MutationTaster	Benign	1.0	N;N;N;N
PrimateAI	Benign	0.35	T
PROVEAN	Benign	-0.11	N
REVEL	Benign	0.0030
Sift	Benign	0.15	T
Sift4G	Benign	0.10	T
Polyphen		0.0	B
Vest4		0.082
MPC		0.0014
ClinPred		0.0051	T
GERP RS		-7.4
Varity_R		0.042
gMVP		0.34

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

Other links and lift over

dbSNP: rs7951297; hg19: chr11-193112; COSMIC: COSV57292562; COSMIC: COSV57292562;