rs4580814

Positions:

• chr5-1113129-G-T

Variant summary

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

The XM_011513941.3(SLC12A7):​c.194-18881C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,066 control chromosomes in the GnomAD database, including 18,322 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 0.47 (18322 hom., cov: 32)
• Consequence: SLC12A7 XM_011513941.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

Genes affected

SLC12A7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC12A7	XM_011513941.3	c.194-18881C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71129 AN: 151946 Hom.: 18321 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.468 AC: 71153 AN: 152066 Hom.: 18322 Cov.: 32 AF XY: 0.466 AC XY: 34635 AN XY: 74336

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.468

Alfa AF: 0.555 Hom.: 44804

Bravo AF: 0.440

Asia WGS AF: 0.332 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4580814; hg19: chr5-1113244;