rs1165209

Variant names:

• chr6-25801091-G-A
• rs1165209
• NM_005074.5:c.1179-111C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-25801091-G-A
• chr6-25801091-G-T

Variant summary

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

The NM_005074.5(SLC17A1):​c.1179-111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 659,366 control chromosomes in the GnomAD database, including 125,279 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 0.66 (35052 hom., cov: 33)
  • Exomes 𝑓: 0.59 (90227 hom.)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 17 publications found

Genes affected

SLC17A1 (HGNC:10929): (solute carrier family 17 member 1) Predicted to enable sialic acid transmembrane transporter activity. Involved in urate metabolic process and urate transport. Located in apical plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005074.5. 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
	SLC17A1	NM_005074.5	MANE Select	c.1179-111C>T		intron	N/A	NP_005065.2	Q14916-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC17A1	ENST00000244527.10	TSL:5 MANE Select	c.1179-111C>T		intron	N/A	ENSP00000244527.4	Q14916-1
	SLC17A1	ENST00000468082.1	TSL:1	c.1017-111C>T		intron	N/A	ENSP00000420546.1	Q14916-2
	SLC17A1	ENST00000476801.5	TSL:2	c.1179-111C>T		intron	N/A	ENSP00000420614.1	Q14916-1

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100544 AN: 151998 Hom.: 34991 Cov.: 33

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.661

GnomAD4 exome AF: 0.586 AC: 297291 AN: 507250 Hom.: 90227 AF XY: 0.580 AC XY: 156911 AN XY: 270758

African (AFR) AF: 0.882 AC: 11826 AN: 13406

American (AMR) AF: 0.698 AC: 16702 AN: 23914

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 7425 AN: 15476

East Asian (EAS) AF: 0.845 AC: 26536 AN: 31390

South Asian (SAS) AF: 0.531 AC: 25202 AN: 47450

European-Finnish (FIN) AF: 0.625 AC: 27020 AN: 43206

Middle Eastern (MID) AF: 0.554 AC: 1156 AN: 2088

European-Non Finnish (NFE) AF: 0.545 AC: 164817 AN: 302522

Other (OTH) AF: 0.597 AC: 16607 AN: 27798

GnomAD4 genome AF: 0.662 AC: 100666 AN: 152116 Hom.: 35052 Cov.: 33 AF XY: 0.663 AC XY: 49329 AN XY: 74356

African (AFR) AF: 0.873 AC: 36266 AN: 41528

American (AMR) AF: 0.655 AC: 10011 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1594 AN: 3472

East Asian (EAS) AF: 0.832 AC: 4311 AN: 5182

South Asian (SAS) AF: 0.530 AC: 2557 AN: 4820

European-Finnish (FIN) AF: 0.643 AC: 6780 AN: 10546

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37277 AN: 67962

Other (OTH) AF: 0.661 AC: 1396 AN: 2112

Alfa AF: 0.585 Hom.: 36973

Bravo AF: 0.678

Asia WGS AF: 0.680 AC: 2368 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	0.083
DANN	Benign	0.62
PhyloP100		-0.82
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: rs1165209; hg19: chr6-25801319;