NM_020689.4:c.142+14084T>C

Variant names:

• chr20-19227068-T-C
• rs8122970
• NM_020689.4:c.142+14084T>C

Variant summary

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

The NM_020689.4(SLC24A3):​c.142+14084T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0681 in 152,234 control chromosomes in the GnomAD database, including 462 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 0.068 (462 hom., cov: 33)
• Consequence: SLC24A3 NM_020689.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.965
• Publications: 2 publications found

Genes affected

SLC24A3 (HGNC:10977): (solute carrier family 24 member 3) Plasma membrane sodium/calcium exchangers are an important component of intracellular calcium homeostasis and electrical conduction. Potassium-dependent sodium/calcium exchangers such as SLC24A3 are believed to transport 1 intracellular calcium and 1 potassium ion in exchange for 4 extracellular sodium ions (Kraev et al., 2001 [PubMed 11294880]).[supplied by OMIM, Mar 2008]

LOC124904879 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC24A3	NM_020689.4	c.142+14084T>C		intron_variant	Intron 1 of 16	ENST00000328041.11	NP_065740.2
LOC124904879	XR_007067552.1	n.3754+72T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC24A3	ENST00000328041.11	c.142+14084T>C		intron_variant	Intron 1 of 16	1	NM_020689.4	ENSP00000333519.5

Frequencies

GnomAD3 genomes AF: 0.0682 AC: 10381 AN: 152116 Hom.: 463 Cov.: 33

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0761

Gnomad SAS AF: 0.0608

Gnomad FIN AF: 0.0464

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0907

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.0681 AC: 10374 AN: 152234 Hom.: 462 Cov.: 33 AF XY: 0.0672 AC XY: 4999 AN XY: 74432

African (AFR) AF: 0.0181 AC: 753 AN: 41564

American (AMR) AF: 0.102 AC: 1553 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3468

East Asian (EAS) AF: 0.0757 AC: 392 AN: 5176

South Asian (SAS) AF: 0.0608 AC: 293 AN: 4816

European-Finnish (FIN) AF: 0.0464 AC: 492 AN: 10606

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0907 AC: 6165 AN: 67996

Other (OTH) AF: 0.0957 AC: 202 AN: 2110

Alfa AF: 0.0676 Hom.: 49

Bravo AF: 0.0711

Asia WGS AF: 0.0740 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	6.4
DANN	Benign	0.75
PhyloP100		0.96
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8122970; hg19: chr20-19207712;