5-128012123-G-A

Variant names:

• chr5-128012123-G-A
• rs1003136
• ENST00000499346.8:n.471+49021C>T

Variant summary

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

The ENST00000499346.8(SLC12A2-DT):​n.471+49021C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,040 control chromosomes in the GnomAD database, including 8,200 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 0.32 (8200 hom., cov: 32)
• Consequence: SLC12A2-DT ENST00000499346.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 12 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 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.543-45195C>T		intron	N/A
	SLC12A2-DT	NR_152802.1		n.308-45195C>T		intron	N/A
	SLC12A2-DT	NR_152803.1		n.442-45195C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC12A2-DT	ENST00000499346.8	TSL:1	n.471+49021C>T		intron	N/A
	SLC12A2-DT	ENST00000514409.7	TSL:1	n.246+49021C>T		intron	N/A
	SLC12A2-DT	ENST00000501173.7	TSL:5	n.570-45195C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49144 AN: 151922 Hom.: 8200 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.323 AC: 49162 AN: 152040 Hom.: 8200 Cov.: 32 AF XY: 0.319 AC XY: 23737 AN XY: 74298

African (AFR) AF: 0.257 AC: 10653 AN: 41480

American (AMR) AF: 0.297 AC: 4527 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1350 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2317 AN: 5158

South Asian (SAS) AF: 0.385 AC: 1853 AN: 4812

European-Finnish (FIN) AF: 0.258 AC: 2724 AN: 10564

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24551 AN: 67978

Other (OTH) AF: 0.353 AC: 744 AN: 2110

Alfa AF: 0.351 Hom.: 37573

Bravo AF: 0.323

Asia WGS AF: 0.411 AC: 1430 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.96
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1003136; hg19: chr5-127347815;