chr5-128006580-C-T

Variant names:

• chr5-128006580-C-T
• rs17164449
• ENST00000499346.8:n.472-49659G>A

Variant summary

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

The ENST00000499346.8(SLC12A2-DT):​n.472-49659G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,000 control chromosomes in the GnomAD database, including 4,249 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 0.23 (4249 hom., cov: 32)
• Consequence: SLC12A2-DT ENST00000499346.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 1 publications found

Genes affected

SLC12A2-DT (HGNC:49565): (SLC12A2 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499346.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC12A2-DT	NR_152798.1		n.543-39652G>A		intron	N/A
	SLC12A2-DT	NR_152802.1		n.308-39652G>A		intron	N/A
	SLC12A2-DT	NR_152803.1		n.442-39652G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC12A2-DT	ENST00000499346.8	TSL:1	n.472-49659G>A		intron	N/A
	SLC12A2-DT	ENST00000514409.7	TSL:1	n.247-49659G>A		intron	N/A
	SLC12A2-DT	ENST00000501173.7	TSL:5	n.570-39652G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34897 AN: 151882 Hom.: 4241 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0451

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.230 AC: 34925 AN: 152000 Hom.: 4249 Cov.: 32 AF XY: 0.224 AC XY: 16618 AN XY: 74290

African (AFR) AF: 0.268 AC: 11104 AN: 41432

American (AMR) AF: 0.181 AC: 2771 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 803 AN: 3470

East Asian (EAS) AF: 0.0452 AC: 234 AN: 5180

South Asian (SAS) AF: 0.170 AC: 818 AN: 4814

European-Finnish (FIN) AF: 0.188 AC: 1979 AN: 10550

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16446 AN: 67950

Other (OTH) AF: 0.229 AC: 482 AN: 2108

Alfa AF: 0.243 Hom.: 924

Bravo AF: 0.231

Asia WGS AF: 0.140 AC: 488 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.062
DANN	Benign	0.39
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs17164449; hg19: chr5-127342272; COSMIC: COSV72287794;