11-193863-T-C

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.207T>C(p.Cys69=) 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 Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.42 (9761 hom., cov: 22)
  • Exomes 𝑓: 0.33 (95531 hom.)
  • Failed GnomAD Quality Control
• Consequence: SCGB1C1 NM_145651.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0850

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=-0.67).
• BP6: Variant 11-193863-T-C is Benign according to our data. Variant chr11-193863-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 768406.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.085 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCGB1C1	NM_145651.3	c.207T>C	p.Cys69=	synonymous_variant	2/3	ENST00000342878.3
SCGB1C1	XM_005252804.4	c.336T>C	p.Cys112=	synonymous_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCGB1C1	ENST00000342878.3	c.207T>C	p.Cys69=	synonymous_variant	2/3	1	NM_145651.3	P1
BET1L	ENST00000410108.5	c.168+11748A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 46365 AN: 110872 Hom.: 9737 Cov.: 22 FAILED QC

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.302

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.395

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.325 AC: 326273 AN: 1002696 Hom.: 95531 Cov.: 33 AF XY: 0.333 AC XY: 168109 AN XY: 504240

Gnomad4 AFR exome AF: 0.204

Gnomad4 AMR exome AF: 0.545

Gnomad4 ASJ exome AF: 0.235

Gnomad4 EAS exome AF: 0.672

Gnomad4 SAS exome AF: 0.498

Gnomad4 FIN exome AF: 0.415

Gnomad4 NFE exome AF: 0.288

Gnomad4 OTH exome AF: 0.343

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.418 AC: 46428 AN: 110986 Hom.: 9761 Cov.: 22 AF XY: 0.420 AC XY: 22340 AN XY: 53166

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.391

Alfa AF: 0.506 Hom.: 3116

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	4.2
Dann	Benign	0.63

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: rs2294081; hg19: chr11-193863; COSMIC: COSV57292326; COSMIC: COSV57292326;