chr22-32349929-C-T

Variant names:

• chr22-32349929-C-T
• rs5998432
• ENST00000701275.2:n.402+2909G>A

Variant summary

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

The ENST00000701275.2(ENSG00000289873):​n.402+2909G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,234 control chromosomes in the GnomAD database, including 1,305 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 0.12 (1305 hom., cov: 32)
• Consequence: ENSG00000289873 ENST00000701275.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 12 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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC5A4	XM_017028920.2	c.107+2948G>A		intron_variant	Intron 2 of 16		XP_016884409.1
SLC5A4	XM_006724308.4	c.-4+2909G>A		intron_variant	Intron 2 of 15		XP_006724371.1
SLC5A4	XM_011530342.3	c.-122+2909G>A		intron_variant	Intron 2 of 16		XP_011528644.1
SLC5A4	XM_011530343.3	c.-4+2948G>A		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.402+2909G>A		intron_variant	Intron 2 of 2
ENSG00000289873	ENST00000701728.2	n.232+2948G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18830 AN: 152116 Hom.: 1296 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0982

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0494

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.124 AC: 18875 AN: 152234 Hom.: 1305 Cov.: 32 AF XY: 0.121 AC XY: 9008 AN XY: 74432

African (AFR) AF: 0.167 AC: 6923 AN: 41520

American (AMR) AF: 0.163 AC: 2498 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0982 AC: 341 AN: 3472

East Asian (EAS) AF: 0.0235 AC: 122 AN: 5186

South Asian (SAS) AF: 0.167 AC: 806 AN: 4816

European-Finnish (FIN) AF: 0.0494 AC: 524 AN: 10610

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7276 AN: 68026

Other (OTH) AF: 0.136 AC: 288 AN: 2112

Alfa AF: 0.115 Hom.: 3423

Bravo AF: 0.132

Asia WGS AF: 0.134 AC: 467 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	1.7
DANN	Benign	0.29
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs5998432; hg19: chr22-32745916;