rs6426327

Variant names:

• chr1-245926509-G-A
• rs6426327
• NM_001167740.2:c.702+1422C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-245926509-G-A
• chr1-245926509-G-C

Variant summary

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

The NM_001167740.2(SMYD3):​c.702+1422C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,088 control chromosomes in the GnomAD database, including 41,078 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 0.69 (41078 hom., cov: 32)
• Consequence: SMYD3 NM_001167740.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.547
• Publications: 17 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001167740.2. 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
	SMYD3	NM_001167740.2	MANE Select	c.702+1422C>T		intron	N/A	NP_001161212.1	Q9H7B4-1
	SMYD3	NM_001375962.1		c.702+1422C>T		intron	N/A	NP_001362891.1
	SMYD3	NM_001375963.1		c.525+1422C>T		intron	N/A	NP_001362892.1	Q9H7B4-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMYD3	ENST00000490107.6	TSL:1 MANE Select	c.702+1422C>T		intron	N/A	ENSP00000419184.2	Q9H7B4-1
	SMYD3	ENST00000366516.5	TSL:1	n.1057+1422C>T		intron	N/A
	SMYD3	ENST00000366517.5	TSL:1	n.566+1422C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104732 AN: 151970 Hom.: 41077 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.689 AC: 104748 AN: 152088 Hom.: 41078 Cov.: 32 AF XY: 0.688 AC XY: 51184 AN XY: 74356

African (AFR) AF: 0.307 AC: 12744 AN: 41450

American (AMR) AF: 0.766 AC: 11709 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3057 AN: 3470

East Asian (EAS) AF: 0.424 AC: 2188 AN: 5162

South Asian (SAS) AF: 0.642 AC: 3091 AN: 4818

European-Finnish (FIN) AF: 0.860 AC: 9104 AN: 10592

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.886 AC: 60251 AN: 67998

Other (OTH) AF: 0.720 AC: 1523 AN: 2114

Alfa AF: 0.831 Hom.: 93672

Bravo AF: 0.665

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.3
DANN	Benign	0.37
PhyloP100		0.55
Mutation Taster		=100/0	polymorphism (auto)

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: rs6426327; hg19: chr1-246089811; COSMIC: COSV100830617;