5-127991957-C-T

Position:

• chr5-127991957-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.308-35036G>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 0.074 in 152,052 control chromosomes in the GnomAD database, including 842 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 0.074 (842 hom., cov: 32)
• Consequence: SLC12A2-DT NR_152813.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

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 = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC12A2-DT	NR_152813.1	n.308-35036G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC12A2-DT	ENST00000499346.7	n.468-35036G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0738 AC: 11218 AN: 151934 Hom.: 836 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0384

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.0800

Gnomad FIN AF: 0.0448

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0172

Gnomad OTH AF: 0.0646

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

GnomAD4 genome AF: 0.0740 AC: 11245 AN: 152052 Hom.: 842 Cov.: 32 AF XY: 0.0789 AC XY: 5865 AN XY: 74312

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0384

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.0803

Gnomad4 FIN AF: 0.0448

Gnomad4 NFE AF: 0.0171

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0286 Hom.: 219

Bravo AF: 0.0862

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs763880; hg19: chr5-127327649;