rs4580814

Variant names:

• chr5-1113129-G-T
• rs4580814
• ENST00000779275.1:n.229-1491G>T

Variant summary

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

The ENST00000779275.1(ENSG00000301492):​n.229-1491G>T 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: ENSG00000301492 ENST00000779275.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 40 publications found

Genes affected

ENSG00000301492 (HGNC:):

SLC12A7 (HGNC:10915): (solute carrier family 12 member 7) Enables protein kinase binding activity. Predicted to be involved in several processes, including cell volume homeostasis; inorganic ion homeostasis; and inorganic ion transmembrane transport. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779275.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301492	ENST00000779275.1		n.229-1491G>T		intron	N/A

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

African (AFR) AF: 0.266 AC: 11049 AN: 41468

American (AMR) AF: 0.408 AC: 6237 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1557 AN: 3472

East Asian (EAS) AF: 0.326 AC: 1675 AN: 5138

South Asian (SAS) AF: 0.452 AC: 2184 AN: 4828

European-Finnish (FIN) AF: 0.615 AC: 6514 AN: 10588

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40364 AN: 67960

Other (OTH) AF: 0.468 AC: 988 AN: 2112

Alfa AF: 0.541 Hom.: 97810

Bravo AF: 0.440

Asia WGS AF: 0.332 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs4580814; hg19: chr5-1113244;