11-193722-A-G

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_145651.3(SCGB1C1):c.66A>G(p.Thr22=) 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.04

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 Benign. Variant got -7 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_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.04 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCGB1C1	NM_145651.3	c.66A>G	p.Thr22=	synonymous_variant	2/3	ENST00000342878.3
SCGB1C1	XM_005252804.4	c.195A>G	p.Thr65=	synonymous_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCGB1C1	ENST00000342878.3	c.66A>G	p.Thr22=	synonymous_variant	2/3	1	NM_145651.3	P1
BET1L	ENST00000410108.5	c.168+11889T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0266 AC: 3220 AN: 120966 Hom.: 1 Cov.: 29

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.: 1 AF XY: 0.191 AC XY: 23618 AN XY: 123396

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.: 1 Cov.: 34 AF XY: 0.00294 AC XY: 2036 AN XY: 693086

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.: 1 Cov.: 29 AF XY: 0.0290 AC XY: 1712 AN XY: 58936

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.: 0

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
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

Other links and lift over

dbSNP: rs2294082; hg19: chr11-193722; COSMIC: COSV57292361; COSMIC: COSV57292361;