5-127991957-C-T

Variant names:

• chr5-127991957-C-T
• rs763880
• ENST00000499346.8:n.472-35036G>A

Variant summary

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

The ENST00000499346.8(SLC12A2-DT):​n.472-35036G>A variant causes a intron 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 ENST00000499346.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 1 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 = 0.335 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC12A2-DT	NR_152798.1		n.543-25029G>A		intron	N/A
	SLC12A2-DT	NR_152802.1		n.308-25029G>A		intron	N/A
	SLC12A2-DT	NR_152803.1		n.442-25029G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC12A2-DT	ENST00000499346.8	TSL:1	n.472-35036G>A		intron	N/A
	SLC12A2-DT	ENST00000514409.7	TSL:1	n.247-35036G>A		intron	N/A
	SLC12A2-DT	ENST00000501173.7	TSL:5	n.570-25029G>A		intron	N/A

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

African (AFR) AF: 0.117 AC: 4838 AN: 41494

American (AMR) AF: 0.152 AC: 2310 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.0384 AC: 133 AN: 3468

East Asian (EAS) AF: 0.348 AC: 1794 AN: 5152

South Asian (SAS) AF: 0.0803 AC: 387 AN: 4820

European-Finnish (FIN) AF: 0.0448 AC: 475 AN: 10604

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0171 AC: 1165 AN: 67976

Other (OTH) AF: 0.0653 AC: 138 AN: 2112

Alfa AF: 0.0391 Hom.: 1080

Bravo AF: 0.0862

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.51
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs763880; hg19: chr5-127327649;