rs17164449

chr5-128006580-C-T

Variant summary

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

The NR_152813.1(SLC12A2-DT):n.308-49659G>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 0.23 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 NR_152813.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC12A2-DT	NR_152813.1	n.308-49659G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC12A2-DT	ENST00000499346.7	n.468-49659G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.0452

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.229

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.062
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

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