Variant chr6-25669555-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_006998.4(SCGN):c.381T>C(p.Ala127Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00423 in 1,613,430 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0035 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0043 ( 27 hom. )

Consequence

SCGN
NM_006998.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.19

Variant links:

Genes affected

SCGN (HGNC:16941): (secretagogin, EF-hand calcium binding protein) The encoded protein is a secreted calcium-binding protein which is found in the cytoplasm. It is related to calbindin D-28K and calretinin. This protein is thought to be involved in KCL-stimulated calcium flux and cell proliferation. [provided by RefSeq, Jul 2008]

SCGN links:

ENSG00000290217 (HGNC:):

ENSG00000290217 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 6-25669555-T-C is Benign according to our data. Variant chr6-25669555-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3024824.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.19 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCGN	NM_006998.4 linkuse as main transcript	c.381T>C	p.Ala127Ala	synonymous_variant	5/11	ENST00000377961.3	NP_008929.2	O76038

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SCGN	ENST00000377961.3 linkuse as main transcript	c.381T>C	p.Ala127Ala	synonymous_variant	5/11	1	NM_006998.4	ENSP00000367197.2	O76038
ENSG00000290217	ENST00000703602.1 linkuse as main transcript	c.381T>C	p.Ala127Ala	synonymous_variant	5/12			ENSP00000515390.1	A0A994J4C2
SCGN	ENST00000612225.4 linkuse as main transcript	n.*160T>C		non_coding_transcript_exon_variant	4/10	5		ENSP00000484392.1	Q96P10
SCGN	ENST00000612225.4 linkuse as main transcript	n.*160T>C		3_prime_UTR_variant	4/10	5		ENSP00000484392.1	Q96P10

Frequencies

GnomAD3 genomes

AF:

0.00349

AC:

531

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00491

Gnomad ASJ

AF:

0.00779

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00495

Gnomad OTH

AF:

0.00525

GnomAD3 exomes

AF:

0.00352

AC:

884

AN:

251462

Hom.:

AF XY:

0.00391

AC XY:

532

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.000800

Gnomad AMR exome

AF:

0.00257

Gnomad ASJ exome

AF:

0.00823

Gnomad EAS exome

AF:

0.00174

Gnomad SAS exome

AF:

0.00385

Gnomad FIN exome

AF:

0.000323

Gnomad NFE exome

AF:

0.00447

Gnomad OTH exome

AF:

0.00538

GnomAD4 exome

AF:

0.00431

AC:

6301

AN:

1461090

Hom.:

Cov.:

AF XY:

0.00439

AC XY:

3191

AN XY:

726714

show subpopulations

Gnomad4 AFR exome

AF:

0.000866

Gnomad4 AMR exome

AF:

0.00318

Gnomad4 ASJ exome

AF:

0.00739

Gnomad4 EAS exome

AF:

0.000907

Gnomad4 SAS exome

AF:

0.00384

Gnomad4 FIN exome

AF:

0.000506

Gnomad4 NFE exome

AF:

0.00466

Gnomad4 OTH exome

AF:

0.00474

GnomAD4 genome

AF:

0.00347

AC:

529

AN:

152340

Hom.:

Cov.:

AF XY:

0.00337

AC XY:

251

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.00101

Gnomad4 AMR

AF:

0.00490

Gnomad4 ASJ

AF:

0.00779

Gnomad4 EAS

AF:

0.00231

Gnomad4 SAS

AF:

0.00352

Gnomad4 FIN

AF:

0.000282

Gnomad4 NFE

AF:

0.00495

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00417

Hom.:

Bravo

AF:

0.00352

Asia WGS

AF:

0.00289

AC:

AN:

3478

EpiCase

AF:

0.00556

EpiControl

AF:

0.00462

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2024

ENSG00000290217: BS2; SCGN: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.8

DANN

Benign

0.51

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