rs1503959

Positions:

• chr14-93399942-C-A
• chr14-93399942-C-T

Variant summary

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

The NM_020818.5(UNC79):​c.-351+66419C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,034 control chromosomes in the GnomAD database, including 38,575 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 0.71 (38575 hom., cov: 31)
• Consequence: UNC79 NM_020818.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

UNC79 (HGNC:19966): (unc-79 homolog, NALCN channel complex subunit) The NALCN channel is responsible for Na(+) leak currents. The protein encoded by this gene, along with UNC80, is an accessory subunit of the NALCN channel that contributes to the Ca(2+) sensitivity of the channel. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UNC79	NM_020818.5	c.-351+66419C>A		intron_variant			NP_065869.3
UNC79	XM_011537027.3	c.-180+66419C>A		intron_variant			XP_011535329.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UNC79	ENST00000256339.8	c.-351+66419C>A		intron_variant		5		ENSP00000256339

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107541 AN: 151916 Hom.: 38549 Cov.: 31

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.708 AC: 107626 AN: 152034 Hom.: 38575 Cov.: 31 AF XY: 0.706 AC XY: 52472 AN XY: 74320

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.743

Alfa AF: 0.688 Hom.: 14334

Bravo AF: 0.717

Asia WGS AF: 0.514 AC: 1787 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.34

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: rs1503959; hg19: chr14-93866288;