Variant 12-50086502-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003076.5(SMARCD1):c.366-119A>G variant causes a intron 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 0.11 ( 337 hom., cov: 0)

Exomes 𝑓: 0.019 ( 249 hom. )

Failed GnomAD Quality Control

Consequence

SMARCD1
NM_003076.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0590

Variant links:

Genes affected

SMARCD1 (HGNC:11106): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1) The protein encoded by this gene is a member of the SWI/SNF family of proteins, whose members display helicase and ATPase activities and which are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI and has sequence similarity to the yeast Swp73 protein. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

SMARCD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 12-50086502-A-G is Benign according to our data. Variant chr12-50086502-A-G is described in ClinVar as [Benign]. Clinvar id is 1220623.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMARCD1	NM_003076.5 linkuse as main transcript	c.366-119A>G		intron_variant		ENST00000394963.9	NP_003067.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMARCD1	ENST00000394963.9 linkuse as main transcript	c.366-119A>G		intron_variant		1	NM_003076.5	ENSP00000378414	P1	Q96GM5-1

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

5422

AN:

49222

Hom.:

330

Cov.:

show subpopulations

Gnomad AFR

AF:

0.293

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0683

Gnomad ASJ

AF:

0.00587

Gnomad EAS

AF:

0.00166

Gnomad SAS

AF:

0.000644

Gnomad FIN

AF:

0.000371

Gnomad MID

AF:

0.0286

Gnomad NFE

AF:

0.00120

Gnomad OTH

AF:

0.0920

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0188

AC:

6620

AN:

351874

Hom.:

249

Cov.:

AF XY:

0.0159

AC XY:

2884

AN XY:

181746

show subpopulations

Gnomad4 AFR exome

AF:

0.276

Gnomad4 AMR exome

AF:

0.0293

Gnomad4 ASJ exome

AF:

0.00596

Gnomad4 EAS exome

AF:

0.00331

Gnomad4 SAS exome

AF:

0.00284

Gnomad4 FIN exome

AF:

0.00174

Gnomad4 NFE exome

AF:

0.0103

Gnomad4 OTH exome

AF:

0.0317

GnomAD4 genome

AF:

0.111

AC:

5453

AN:

49258

Hom.:

337

Cov.:

AF XY:

0.110

AC XY:

2593

AN XY:

23484

show subpopulations

Gnomad4 AFR

AF:

0.294

Gnomad4 AMR

AF:

0.0683

Gnomad4 ASJ

AF:

0.00587

Gnomad4 EAS

AF:

0.00167

Gnomad4 SAS

AF:

0.000646

Gnomad4 FIN

AF:

0.000371

Gnomad4 NFE

AF:

0.00120

Gnomad4 OTH

AF:

0.0908

Alfa

AF:

0.00956

Hom.:

Bravo

AF:

0.0403

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	GeneDx	May 23, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.1

DANN

Benign

0.49

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