rs9728248

Variant names:

• chr1-245842496-C-A
• rs9728248
• NM_001167740.2:c.1076+16000G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-245842496-C-A
• chr1-245842496-C-G

Variant summary

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

The NM_001167740.2(SMYD3):​c.1076+16000G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,916 control chromosomes in the GnomAD database, including 10,532 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 0.35 (10532 hom., cov: 32)
• Consequence: SMYD3 NM_001167740.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707

Genes affected

SMYD3 (HGNC:15513): (SET and MYND domain containing 3) This gene encodes a histone methyltransferase which functions in RNA polymerase II complexes by an interaction with a specific RNA helicase. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMYD3	NM_001167740.2	c.1076+16000G>T		intron_variant	Intron 10 of 11	ENST00000490107.6	NP_001161212.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMYD3	ENST00000490107.6	c.1076+16000G>T		intron_variant	Intron 10 of 11	1	NM_001167740.2	ENSP00000419184.2

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53018 AN: 151798 Hom.: 10502 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.350 AC: 53095 AN: 151916 Hom.: 10532 Cov.: 32 AF XY: 0.360 AC XY: 26720 AN XY: 74232

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.340

Alfa AF: 0.336 Hom.: 4431

Bravo AF: 0.352

Asia WGS AF: 0.703 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.85
DANN	Benign	0.69

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: rs9728248; hg19: chr1-246005798;