5-1057845-C-T

Variant names:

• chr5-1057845-C-T
• rs35791340
• NM_006598.3:c.2848-196G>A

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.2848-196G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,086 control chromosomes in the GnomAD database, including 37,381 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.66 (37381 hom., cov: 32)
• Consequence: SLC12A7 NM_006598.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.370

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=-0.91).
• BP6: Variant 5-1057845-C-T is Benign according to our data. Variant chr5-1057845-C-T is described in ClinVar as [Benign]. Clinvar id is 1287555.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC12A7	NM_006598.3	c.2848-196G>A		intron_variant	Intron 21 of 23	ENST00000264930.10	NP_006589.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC12A7	ENST00000264930.10	c.2848-196G>A		intron_variant	Intron 21 of 23	1	NM_006598.3	ENSP00000264930.5
SLC12A7	ENST00000634447.1	c.2548-196G>A		intron_variant	Intron 19 of 22	5		ENSP00000489285.1
SLC12A7	ENST00000513223.2	c.943-196G>A		intron_variant	Intron 7 of 7	5		ENSP00000428854.2
SLC12A7	ENST00000514994.1	n.148-196G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100700 AN: 151968 Hom.: 37384 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.662 AC: 100707 AN: 152086 Hom.: 37381 Cov.: 32 AF XY: 0.667 AC XY: 49562 AN XY: 74350

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.683

Alfa AF: 0.753 Hom.: 7717

Bravo AF: 0.637

Asia WGS AF: 0.688 AC: 2391 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.49
RBP_binding_hub_radar		0.85
RBP_regulation_power_radar		2.1

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: rs35791340; hg19: chr5-1057960;