3-43340293-C-T

Variant names:

• chr3-43340293-C-T
• rs17075574
• NM_017719.5:c.738C>T

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BA1

The NM_017719.5(SNRK):​c.738C>T​(p.Ile246Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00503 in 1,613,746 control chromosomes in the GnomAD database, including 318 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.025 (160 hom., cov: 31)
  • Exomes 𝑓: 0.0030 (158 hom.)
• Consequence: SNRK NM_017719.5 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.239
• Publications: 1 publications found

Genes affected

SNRK (HGNC:30598): (SNF related kinase) SNRK is a member of the sucrose nonfermenting (SNF)-related kinase family of serine/threonine kinases (Kertesz et al., 2002 [PubMed 12234663]).[supplied by OMIM, Apr 2009]

ACMG classification

Our verdict: Benign. The variant received -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BP6: Variant 3-43340293-C-T is Benign according to our data. Variant chr3-43340293-C-T is described in ClinVar as Benign. ClinVar VariationId is 791919.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.239 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017719.5. 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
	SNRK	NM_017719.5	MANE Select	c.738C>T	p.Ile246Ile	synonymous	Exon 5 of 7	NP_060189.3
	SNRK	NM_001100594.2		c.738C>T	p.Ile246Ile	synonymous	Exon 4 of 6	NP_001094064.1	Q9NRH2-1
	SNRK	NM_001330750.2		c.120C>T	p.Ile40Ile	synonymous	Exon 3 of 5	NP_001317679.1	E7EUC4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNRK	ENST00000296088.12	TSL:1 MANE Select	c.738C>T	p.Ile246Ile	synonymous	Exon 5 of 7	ENSP00000296088.7	Q9NRH2-1
	SNRK	ENST00000429705.6	TSL:1	c.738C>T	p.Ile246Ile	synonymous	Exon 4 of 6	ENSP00000411375.2	Q9NRH2-1
	SNRK	ENST00000454177.5	TSL:2	c.738C>T	p.Ile246Ile	synonymous	Exon 6 of 8	ENSP00000401246.1	Q9NRH2-1

Frequencies

GnomAD3 genomes AF: 0.0250 AC: 3796 AN: 152142 Hom.: 159 Cov.: 31

Gnomad AFR AF: 0.0846

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0117

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000514

Gnomad OTH AF: 0.0186

GnomAD2 exomes AF: 0.00699 AC: 1743 AN: 249520 AF XY: 0.00554

Gnomad AFR exome AF: 0.0871

Gnomad AMR exome AF: 0.00501

Gnomad ASJ exome AF: 0.0118

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000556

Gnomad OTH exome AF: 0.00594

GnomAD4 exome AF: 0.00295 AC: 4318 AN: 1461486 Hom.: 158 Cov.: 30 AF XY: 0.00263 AC XY: 1909 AN XY: 727092

African (AFR) AF: 0.0884 AC: 2956 AN: 33450

American (AMR) AF: 0.00595 AC: 266 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.0113 AC: 294 AN: 26128

East Asian (EAS) AF: 0.00 AC: 0 AN: 39694

South Asian (SAS) AF: 0.0000696 AC: 6 AN: 86198

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53404

Middle Eastern (MID) AF: 0.00416 AC: 24 AN: 5768

European-Non Finnish (NFE) AF: 0.000327 AC: 363 AN: 1111742

Other (OTH) AF: 0.00677 AC: 409 AN: 60380

GnomAD4 genome AF: 0.0250 AC: 3803 AN: 152260 Hom.: 160 Cov.: 31 AF XY: 0.0239 AC XY: 1778 AN XY: 74452

African (AFR) AF: 0.0846 AC: 3512 AN: 41532

American (AMR) AF: 0.0116 AC: 178 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.000414 AC: 2 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000515 AC: 35 AN: 68026

Other (OTH) AF: 0.0184 AC: 39 AN: 2114

Alfa AF: 0.0130 Hom.: 64

Bravo AF: 0.0294

Asia WGS AF: 0.00549 AC: 19 AN: 3478

EpiCase AF: 0.000818

EpiControl AF: 0.000771

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	8.7
DANN	Benign	0.74
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs17075574; hg19: chr3-43381785;