17-18959230-C-T

Variant names:

• chr17-18959230-C-T
• rs146918144
• NM_001042450.4:c.279C>T

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_Moderate BP7 BS2

The NM_001042450.4(SLC5A10):​c.279C>T​(p.Phe93Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00115 in 1,612,986 control chromosomes in the GnomAD database, including 4 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 0.00075 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0012 (4 hom.)
• Consequence: SLC5A10 NM_001042450.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 1 publications found

Genes affected

SLC5A10 (HGNC:23155): (solute carrier family 5 member 10) This gene is a member of the sodium/glucose transporter family. Members of this family are sodium-dependent transporters and can be divided into two subfamilies based on sequence homology, one that co-transports sugars and the second that transports molecules such as ascorbate, choline, iodide, lipoate, monocaroboxylates, and pantothenate. The protein encoded by this gene has the highest affinity for mannose and has been reported to be most highly expressed in the kidney. This protein may function as a kidney-specific, sodium-dependent mannose and fructose co-transporter. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Benign. The variant received -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BP7: Synonymous conserved (PhyloP=-1.08 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 4 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001042450.4. 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
	SLC5A10	NM_001042450.4	MANE Select	c.279C>T	p.Phe93Phe	synonymous	Exon 3 of 15	NP_001035915.1	A0PJK1-1
	SLC5A10	NM_152351.6		c.279C>T	p.Phe93Phe	synonymous	Exon 3 of 15	NP_689564.3
	SLC5A10	NM_001270648.3		c.279C>T	p.Phe93Phe	synonymous	Exon 3 of 14	NP_001257577.1	A0PJK1-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC5A10	ENST00000395645.4	TSL:1 MANE Select	c.279C>T	p.Phe93Phe	synonymous	Exon 3 of 15	ENSP00000379007.3	A0PJK1-1
	SLC5A10	ENST00000395643.6	TSL:1	c.279C>T	p.Phe93Phe	synonymous	Exon 3 of 14	ENSP00000379005.2	A0PJK1-2
	SLC5A10	ENST00000317977.10	TSL:1	c.111C>T	p.Phe37Phe	synonymous	Exon 3 of 15	ENSP00000324346.6	A0PJK1-3

Frequencies

GnomAD3 genomes AF: 0.000749 AC: 114 AN: 152192 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000393

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00141

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.00102 AC: 255 AN: 249332 AF XY: 0.000917

Gnomad AFR exome AF: 0.000313

Gnomad AMR exome AF: 0.000550

Gnomad ASJ exome AF: 0.000200

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000142

Gnomad NFE exome AF: 0.00183

Gnomad OTH exome AF: 0.000988

GnomAD4 exome AF: 0.00119 AC: 1744 AN: 1460794 Hom.: 4 Cov.: 32 AF XY: 0.00116 AC XY: 841 AN XY: 726754

African (AFR) AF: 0.000239 AC: 8 AN: 33466

American (AMR) AF: 0.000537 AC: 24 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.0000765 AC: 2 AN: 26128

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.000661 AC: 57 AN: 86228

European-Finnish (FIN) AF: 0.000512 AC: 27 AN: 52696

Middle Eastern (MID) AF: 0.00216 AC: 12 AN: 5558

European-Non Finnish (NFE) AF: 0.00139 AC: 1551 AN: 1111946

Other (OTH) AF: 0.00104 AC: 63 AN: 60352

GnomAD4 genome AF: 0.000749 AC: 114 AN: 152192 Hom.: 0 Cov.: 33 AF XY: 0.000659 AC XY: 49 AN XY: 74338

African (AFR) AF: 0.000193 AC: 8 AN: 41456

American (AMR) AF: 0.000393 AC: 6 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5198

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4826

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10610

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00141 AC: 96 AN: 68034

Other (OTH) AF: 0.00 AC: 0 AN: 2094

Alfa AF: 0.000839 Hom.: 1

Bravo AF: 0.000805

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.00104

EpiControl AF: 0.00166

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	4.3
DANN	Benign	0.87
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

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: rs146918144; hg19: chr17-18862543; COSMIC: COSV58757094;