17-63832807-G-C

Variant names:

• chr17-63832807-G-C
• rs2584622
• NM_001098426.2:c.*131C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001098426.2(SMARCD2):​c.*131C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SMARCD2 NM_001098426.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 14 publications found

Genes affected

SMARCD2 (HGNC:11107): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2) 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. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

SMARCD2 Gene-Disease associations (from GenCC):

• specific granule deficiency 2

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• specific granule deficiency

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCD2	NM_001098426.2	c.*131C>G		3_prime_UTR_variant	Exon 13 of 13	ENST00000448276.7	NP_001091896.1
SMARCD2	NM_001330440.2	c.*131C>G		3_prime_UTR_variant	Exon 13 of 13		NP_001317369.1
SMARCD2	NM_001330439.1	c.*131C>G		3_prime_UTR_variant	Exon 13 of 13		NP_001317368.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCD2	ENST00000448276.7	c.*131C>G		3_prime_UTR_variant	Exon 13 of 13	1	NM_001098426.2	ENSP00000392617.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 617972 Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0 AN XY: 324420

African (AFR) AF: 0.00 AC: 0 AN: 15968

American (AMR) AF: 0.00 AC: 0 AN: 29246

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18288

East Asian (EAS) AF: 0.00 AC: 0 AN: 31842

South Asian (SAS) AF: 0.00 AC: 0 AN: 59614

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45984

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2466

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 382920

Other (OTH) AF: 0.00 AC: 0 AN: 31644

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 67226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.3
DANN	Benign	0.55
PhyloP100		1.4

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

Other links and lift over

dbSNP: rs2584622; hg19: chr17-61910167;