chr6-25823216-A-T

Position:

• chr6-25823216-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005074.5(SLC17A1):​c.207+3245T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,016 control chromosomes in the GnomAD database, including 33,863 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 0.65 (33863 hom., cov: 32)
• Consequence: SLC17A1 NM_005074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC17A1	NM_005074.5	c.207+3245T>A		intron_variant		ENST00000244527.10	NP_005065.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC17A1	ENST00000244527.10	c.207+3245T>A		intron_variant		5	NM_005074.5	ENSP00000244527.4
SLC17A1	ENST00000468082.1	c.207+3245T>A		intron_variant		1		ENSP00000420546.1
SLC17A1	ENST00000476801.5	c.207+3245T>A		intron_variant		2		ENSP00000420614.1
SLC17A1	ENST00000377886.6	n.207+3245T>A		intron_variant		5		ENSP00000367118.2

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98577 AN: 151898 Hom.: 33804 Cov.: 32

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.645

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.649 AC: 98698 AN: 152016 Hom.: 33863 Cov.: 32 AF XY: 0.650 AC XY: 48303 AN XY: 74292

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.646

Alfa AF: 0.558 Hom.: 13450

Bravo AF: 0.667

Asia WGS AF: 0.671 AC: 2334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.62

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

Publications

LitVar

Other links and lift over

dbSNP: rs1183201; hg19: chr6-25823444;