NM_001167740.2:c.164+9120G>A

Variant names:

• chr1-246497934-C-T
• rs11800820
• NM_001167740.2:c.164+9120G>A

Variant summary

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

The NM_001167740.2(SMYD3):​c.164+9120G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,518 control chromosomes in the GnomAD database, including 7,361 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 0.31 (7361 hom., cov: 32)
• Consequence: SMYD3 NM_001167740.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMYD3	NM_001167740.2	MANE Select	c.164+9120G>A		intron	N/A	NP_001161212.1
	SMYD3	NM_001375962.1		c.164+9120G>A		intron	N/A	NP_001362891.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMYD3	ENST00000490107.6	TSL:1 MANE Select	c.164+9120G>A		intron	N/A	ENSP00000419184.2
	SMYD3	ENST00000403792.7	TSL:1	c.164+9120G>A		intron	N/A	ENSP00000385380.3
	SMYD3	ENST00000462422.5	TSL:5	n.91+9120G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46495 AN: 151406 Hom.: 7349 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.0578

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.307 AC: 46530 AN: 151518 Hom.: 7361 Cov.: 32 AF XY: 0.303 AC XY: 22408 AN XY: 74042

African (AFR) AF: 0.294 AC: 12146 AN: 41362

American (AMR) AF: 0.281 AC: 4275 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1358 AN: 3468

East Asian (EAS) AF: 0.0579 AC: 299 AN: 5162

South Asian (SAS) AF: 0.264 AC: 1269 AN: 4810

European-Finnish (FIN) AF: 0.306 AC: 3178 AN: 10376

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22764 AN: 67798

Other (OTH) AF: 0.326 AC: 683 AN: 2098

Alfa AF: 0.328 Hom.: 21263

Bravo AF: 0.300

Asia WGS AF: 0.160 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.30
PhyloP100		0.30
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: rs11800820; hg19: chr1-246661236;