NM_001199633.2:c.669+124T>C

Variant names:

• chr9-84299457-A-G
• rs17087049
• NM_001199633.2:c.669+124T>C

Variant summary

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

The NM_001199633.2(SLC28A3):​c.669+124T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0408 in 1,273,650 control chromosomes in the GnomAD database, including 5,172 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 0.11 (2041 hom., cov: 32)
  • Exomes 𝑓: 0.032 (3131 hom.)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 4 publications found

Genes affected

SLC28A3 (HGNC:16484): (solute carrier family 28 member 3) Nucleoside transporters, such as SLC28A3, regulate multiple cellular processes, including neurotransmission, vascular tone, adenosine concentration in the vicinity of cell surface receptors, and transport and metabolism of nucleoside drugs. SLC28A3 shows broad specificity for pyrimidine and purine nucleosides (Ritzel et al., 2001 [PubMed 11032837]).[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199633.2. 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
	SLC28A3	NM_001199633.2	MANE Select	c.669+124T>C		intron	N/A	NP_001186562.1
	SLC28A3	NM_022127.3		c.669+124T>C		intron	N/A	NP_071410.1
	SLC28A3	NR_037638.3		n.970+124T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A3	ENST00000376238.5	TSL:1 MANE Select	c.669+124T>C		intron	N/A	ENSP00000365413.4

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16317 AN: 152098 Hom.: 2026 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.0866

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00870

Gnomad OTH AF: 0.0765

GnomAD4 exome AF: 0.0318 AC: 35640 AN: 1121434 Hom.: 3131 AF XY: 0.0320 AC XY: 17957 AN XY: 560954

African (AFR) AF: 0.301 AC: 7393 AN: 24594

American (AMR) AF: 0.161 AC: 4108 AN: 25558

Ashkenazi Jewish (ASJ) AF: 0.00939 AC: 185 AN: 19710

East Asian (EAS) AF: 0.266 AC: 9177 AN: 34562

South Asian (SAS) AF: 0.0825 AC: 5147 AN: 62396

European-Finnish (FIN) AF: 0.0167 AC: 691 AN: 41324

Middle Eastern (MID) AF: 0.0245 AC: 94 AN: 3830

European-Non Finnish (NFE) AF: 0.00770 AC: 6629 AN: 860992

Other (OTH) AF: 0.0457 AC: 2216 AN: 48468

GnomAD4 genome AF: 0.108 AC: 16371 AN: 152216 Hom.: 2041 Cov.: 32 AF XY: 0.109 AC XY: 8095 AN XY: 74430

African (AFR) AF: 0.287 AC: 11909 AN: 41502

American (AMR) AF: 0.114 AC: 1741 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3472

East Asian (EAS) AF: 0.262 AC: 1355 AN: 5166

South Asian (SAS) AF: 0.0867 AC: 418 AN: 4822

European-Finnish (FIN) AF: 0.0164 AC: 174 AN: 10624

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00869 AC: 591 AN: 68032

Other (OTH) AF: 0.0752 AC: 159 AN: 2114

Alfa AF: 0.0481 Hom.: 2422

Bravo AF: 0.127

Asia WGS AF: 0.153 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.8
DANN	Benign	0.64
PhyloP100		0.15
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: rs17087049; hg19: chr9-86914372; COSMIC: COSV107496272;