rs1003136

Variant names:

• chr5-128012123-G-A
• rs1003136
• ENST00000499346.7:n.467+49021C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-128012123-G-A
• chr5-128012123-G-C
• chr5-128012123-G-T

Variant summary

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

The ENST00000499346.7(SLC12A2-DT):​n.467+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 ENST00000499346.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC12A2-DT	NR_152798.1	n.543-45195C>T		intron_variant	Intron 2 of 2
SLC12A2-DT	NR_152802.1	n.308-45195C>T		intron_variant	Intron 2 of 2
SLC12A2-DT	NR_152803.1	n.442-45195C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC12A2-DT	ENST00000499346.7	n.467+49021C>T		intron_variant	Intron 2 of 3	1
SLC12A2-DT	ENST00000514409.6	n.229+49021C>T		intron_variant	Intron 2 of 3	1
SLC12A2-DT	ENST00000501173.6	n.570-45195C>T		intron_variant	Intron 3 of 3	5

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

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.353

Alfa AF: 0.351 Hom.: 16502

Bravo AF: 0.323

Asia WGS AF: 0.411 AC: 1430 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1003136; hg19: chr5-127347815;