rs5753917

Variant names:

• chr22-32287178-G-A
• rs5753917
• ENST00000701275.2:n.403-20826C>T

Variant summary

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

The ENST00000701275.2(ENSG00000289873):​n.403-20826C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,012 control chromosomes in the GnomAD database, including 6,124 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 0.28 (6124 hom., cov: 32)
• Consequence: ENSG00000289873 ENST00000701275.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• Publications: 2 publications found

Genes affected

ENSG00000289873 (HGNC:):

SLC5A4 (HGNC:11039): (solute carrier family 5 member 4) Predicted to enable glucose:sodium symporter activity and proton transmembrane transporter activity. Predicted to be involved in sodium ion transport. Predicted to act upstream of or within proton transmembrane transport. Predicted to be active in plasma membrane. Predicted to be integral component of 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC5A4	XM_017028920.2	c.108-20826C>T		intron_variant	Intron 2 of 16		XP_016884409.1
SLC5A4	XM_006724308.4	c.-3-32965C>T		intron_variant	Intron 2 of 15		XP_006724371.1
SLC5A4	XM_011530342.3	c.-121-20826C>T		intron_variant	Intron 2 of 16		XP_011528644.1
SLC5A4	XM_011530343.3	c.-3-32965C>T		intron_variant	Intron 1 of 14		XP_011528645.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289873	ENST00000701275.2	n.403-20826C>T		intron_variant	Intron 2 of 2
ENSG00000289873	ENST00000701728.2	n.233-20826C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42916 AN: 151894 Hom.: 6114 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.283 AC: 42949 AN: 152012 Hom.: 6124 Cov.: 32 AF XY: 0.284 AC XY: 21113 AN XY: 74310

African (AFR) AF: 0.324 AC: 13403 AN: 41428

American (AMR) AF: 0.276 AC: 4208 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3468

East Asian (EAS) AF: 0.309 AC: 1600 AN: 5170

South Asian (SAS) AF: 0.304 AC: 1468 AN: 4822

European-Finnish (FIN) AF: 0.331 AC: 3493 AN: 10550

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17223 AN: 67992

Other (OTH) AF: 0.265 AC: 559 AN: 2110

Alfa AF: 0.265 Hom.: 2101

Bravo AF: 0.279

Asia WGS AF: 0.294 AC: 1019 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	0.20
DANN	Benign	0.37
PhyloP100		-0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5753917; hg19: chr22-32683165;