chr3-43303615-A-C

Variant names:

• chr3-43303615-A-C
• rs17075521
• NM_017719.5:c.412A>C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_017719.5(SNRK):​c.412A>C​(p.Arg138Arg) variant causes a synonymous change. The variant allele was found at a frequency of 0.00582 in 1,614,132 control chromosomes in the GnomAD database, including 374 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.028 (203 hom., cov: 32)
  • Exomes 𝑓: 0.0035 (171 hom.)
• Consequence: SNRK NM_017719.5 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 4.80
• Publications: 2 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP6: Variant 3-43303615-A-C is Benign according to our data. Variant chr3-43303615-A-C is described in ClinVar as Benign. ClinVar VariationId is 775863.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0946 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.412A>C	p.Arg138Arg	synonymous	Exon 3 of 7	NP_060189.3
	SNRK	NM_001100594.2		c.412A>C	p.Arg138Arg	synonymous	Exon 2 of 6	NP_001094064.1	Q9NRH2-1
	SNRK	NM_001330750.2		c.-30+16940A>C		intron	N/A	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.412A>C	p.Arg138Arg	synonymous	Exon 3 of 7	ENSP00000296088.7	Q9NRH2-1
	SNRK	ENST00000429705.6	TSL:1	c.412A>C	p.Arg138Arg	synonymous	Exon 2 of 6	ENSP00000411375.2	Q9NRH2-1
	SNRK	ENST00000454177.5	TSL:2	c.412A>C	p.Arg138Arg	synonymous	Exon 4 of 8	ENSP00000401246.1	Q9NRH2-1

Frequencies

GnomAD3 genomes AF: 0.0285 AC: 4335 AN: 152172 Hom.: 203 Cov.: 32

Gnomad AFR AF: 0.0973

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0118

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00110

Gnomad OTH AF: 0.0187

GnomAD2 exomes AF: 0.00774 AC: 1929 AN: 249266 AF XY: 0.00590

Gnomad AFR exome AF: 0.102

Gnomad AMR exome AF: 0.00507

Gnomad ASJ exome AF: 0.00139

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000464

Gnomad NFE exome AF: 0.000893

Gnomad OTH exome AF: 0.00595

GnomAD4 exome AF: 0.00346 AC: 5052 AN: 1461842 Hom.: 171 Cov.: 31 AF XY: 0.00311 AC XY: 2260 AN XY: 727212

African (AFR) AF: 0.0997 AC: 3338 AN: 33476

American (AMR) AF: 0.00593 AC: 265 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00149 AC: 39 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39696

South Asian (SAS) AF: 0.000614 AC: 53 AN: 86250

European-Finnish (FIN) AF: 0.0000374 AC: 2 AN: 53408

Middle Eastern (MID) AF: 0.0127 AC: 73 AN: 5768

European-Non Finnish (NFE) AF: 0.000738 AC: 821 AN: 1111988

Other (OTH) AF: 0.00763 AC: 461 AN: 60396

GnomAD4 genome AF: 0.0285 AC: 4340 AN: 152290 Hom.: 203 Cov.: 32 AF XY: 0.0276 AC XY: 2054 AN XY: 74478

African (AFR) AF: 0.0971 AC: 4034 AN: 41524

American (AMR) AF: 0.0118 AC: 181 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.000622 AC: 3 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

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

European-Non Finnish (NFE) AF: 0.00110 AC: 75 AN: 68032

Other (OTH) AF: 0.0185 AC: 39 AN: 2112

Alfa AF: 0.0125 Hom.: 66

Bravo AF: 0.0319

Asia WGS AF: 0.00635 AC: 23 AN: 3478

EpiCase AF: 0.00224

EpiControl AF: 0.00119

ClinVar

ClinVar submissions as Germline

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	-0.55
CADD	Benign	11
DANN	Benign	0.63
PhyloP100		4.8
Mutation Taster		=99/1	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: rs17075521; hg19: chr3-43345107;