rs146579248

chr5-128046610-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_152813.1(SLC12A2-DT):n.307+14534G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0212 in 152,302 control chromosomes in the GnomAD database, including 51 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 0.021 (51 hom., cov: 33)
• Consequence: SLC12A2-DT NR_152813.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

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=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0212 (3228/152302) while in subpopulation NFE AF= 0.03 (2041/68012). AF 95% confidence interval is 0.0289. There are 51 homozygotes in gnomad4. There are 1547 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 51 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC12A2-DT	NR_152813.1	n.307+14534G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC12A2-DT	ENST00000499346.7	n.467+14534G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0212 AC: 3230 AN: 152184 Hom.: 51 Cov.: 33

Gnomad AFR AF: 0.00487

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.0157

Gnomad ASJ AF: 0.0648

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0300

Gnomad OTH AF: 0.0224

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

GnomAD4 genome AF: 0.0212 AC: 3228 AN: 152302 Hom.: 51 Cov.: 33 AF XY: 0.0208 AC XY: 1547 AN XY: 74484

Gnomad4 AFR AF: 0.00486

Gnomad4 AMR AF: 0.0157

Gnomad4 ASJ AF: 0.0648

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.0155

Gnomad4 NFE AF: 0.0300

Gnomad4 OTH AF: 0.0222

Alfa AF: 0.0298 Hom.: 9

Bravo AF: 0.0202

Asia WGS AF: 0.0220 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.1
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs146579248; hg19: chr5-127382302;