5-1053637-A-G

Variant names:

• chr5-1053637-A-G
• rs80090801
• NM_006598.3:c.3027-155T>C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_006598.3(SLC12A7):​c.3027-155T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,232 control chromosomes in the GnomAD database, including 1,797 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.10 (1797 hom., cov: 34)
• Consequence: SLC12A7 NM_006598.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0330

Genes affected

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

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 5-1053637-A-G is Benign according to our data. Variant chr5-1053637-A-G is described in ClinVar as [Benign]. Clinvar id is 1235255.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC12A7	NM_006598.3	c.3027-155T>C		intron_variant	Intron 22 of 23	ENST00000264930.10	NP_006589.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC12A7	ENST00000264930.10	c.3027-155T>C		intron_variant	Intron 22 of 23	1	NM_006598.3	ENSP00000264930.5
SLC12A7	ENST00000634447.1	c.2742-155T>C		intron_variant	Intron 21 of 22	5		ENSP00000489285.1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15657 AN: 152114 Hom.: 1788 Cov.: 34

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0980

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0391

Gnomad FIN AF: 0.0309

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0160

Gnomad OTH AF: 0.0802

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

GnomAD4 genome AF: 0.103 AC: 15703 AN: 152232 Hom.: 1797 Cov.: 34 AF XY: 0.103 AC XY: 7666 AN XY: 74464

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.0982

Gnomad4 ASJ AF: 0.0588

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0391

Gnomad4 FIN AF: 0.0309

Gnomad4 NFE AF: 0.0160

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.0684 Hom.: 120

Bravo AF: 0.118

Asia WGS AF: 0.119 AC: 413 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs80090801; hg19: chr5-1053752;