rs9308433

Positions:

• chr1-214283666-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020197.3(SMYD2):​c.173+2239T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,994 control chromosomes in the GnomAD database, including 13,997 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 0.41 (13997 hom., cov: 32)
• Consequence: SMYD2 NM_020197.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

Genes affected

SMYD2 (HGNC:20982): (SET and MYND domain containing 2) SET domain-containing proteins, such as SMYD2, catalyze lysine methylation (Brown et al., 2006 [PubMed 16805913]).[supplied by OMIM, Nov 2008]

SMYD2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMYD2	NM_020197.3	c.173+2239T>C		intron_variant		ENST00000366957.10	NP_064582.2
SMYD2	XM_047425700.1	c.-16+2239T>C		intron_variant			XP_047281656.1
SMYD2	XM_047425702.1	c.173+2239T>C		intron_variant			XP_047281658.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMYD2	ENST00000366957.10	c.173+2239T>C		intron_variant		1	NM_020197.3	ENSP00000355924.5
SMYD2	ENST00000460580.5	n.206+2239T>C		intron_variant		1
SMYD2	ENST00000471645.5	n.303+2239T>C		intron_variant		1
SMYD2	ENST00000491455.5	n.326+2239T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62912 AN: 151876 Hom.: 13971 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.0633

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.414 AC: 62987 AN: 151994 Hom.: 13997 Cov.: 32 AF XY: 0.408 AC XY: 30286 AN XY: 74294

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.0632

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.358

Alfa AF: 0.382 Hom.: 14329

Bravo AF: 0.422

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.44

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: rs9308433; hg19: chr1-214457009;