rs1503959

Variant names:

• chr14-93399942-C-A
• rs1503959
• NM_020818.5:c.-351+66419C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

UNC79 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
UNC79	NM_020818.5	c.-351+66419C>A		intron_variant	Intron 1 of 49		NP_065869.3
UNC79	XM_011537027.3	c.-180+66419C>A		intron_variant	Intron 1 of 51		XP_011535329.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UNC79	ENST00000256339.8	c.-351+66419C>A		intron_variant	Intron 1 of 49	5		ENSP00000256339.4

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

African (AFR) AF: 0.755 AC: 31293 AN: 41452

American (AMR) AF: 0.755 AC: 11525 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2446 AN: 3468

East Asian (EAS) AF: 0.345 AC: 1779 AN: 5158

South Asian (SAS) AF: 0.648 AC: 3128 AN: 4826

European-Finnish (FIN) AF: 0.657 AC: 6937 AN: 10562

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47997 AN: 67982

Other (OTH) AF: 0.743 AC: 1570 AN: 2114

Alfa AF: 0.691 Hom.: 16465

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
PhyloP100		-0.068
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: rs1503959; hg19: chr14-93866288;