rs17173769

Variant names:

• chr7-151260343-T-C
• rs17173769
• ENST00000356800.6:c.40-14672A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003078.4(SMARCD3):​c.40-14672A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0313 in 152,282 control chromosomes in the GnomAD database, including 165 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.031 (165 hom., cov: 32)
• Consequence: SMARCD3 NM_003078.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 1 publications found

Genes affected

SMARCD3 (HGNC:11108): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3) 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. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0984 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003078.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMARCD3	NM_001003802.2		c.40-14672A>G		intron	N/A	NP_001003802.1	Q6STE5-2
	SMARCD3	NM_003078.4		c.40-14672A>G		intron	N/A	NP_003069.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMARCD3	ENST00000356800.6	TSL:1	c.40-14672A>G		intron	N/A	ENSP00000349254.2	Q6STE5-2
	SMARCD3	ENST00000392811.6	TSL:1	c.40-14672A>G		intron	N/A	ENSP00000376558.2	Q6STE5-2
	SMARCD3	ENST00000491651.1	TSL:4	c.40-14672A>G		intron	N/A	ENSP00000419886.1	C9JYI7

Frequencies

GnomAD3 genomes AF: 0.0313 AC: 4768 AN: 152162 Hom.: 165 Cov.: 32

Gnomad AFR AF: 0.00700

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.0205

Gnomad FIN AF: 0.0275

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0268

Gnomad OTH AF: 0.0339

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0313 AC: 4768 AN: 152282 Hom.: 165 Cov.: 32 AF XY: 0.0326 AC XY: 2427 AN XY: 74460

African (AFR) AF: 0.00698 AC: 290 AN: 41544

American (AMR) AF: 0.0975 AC: 1491 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 91 AN: 3470

East Asian (EAS) AF: 0.106 AC: 548 AN: 5182

South Asian (SAS) AF: 0.0207 AC: 100 AN: 4824

European-Finnish (FIN) AF: 0.0275 AC: 292 AN: 10624

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0268 AC: 1825 AN: 68030

Other (OTH) AF: 0.0331 AC: 70 AN: 2114

Alfa AF: 0.0364 Hom.: 77

Bravo AF: 0.0379

Asia WGS AF: 0.0400 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.90
DANN	Benign	0.51
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17173769; hg19: chr7-150957429;