rs943323

Positions:

• chr14-93694175-C-A
• chr14-93694175-C-G

Variant summary

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

The NM_001395159.1(UNC79):​c.7804-160C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,080 control chromosomes in the GnomAD database, including 39,196 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 (39196 hom., cov: 32)
• Consequence: UNC79 NM_001395159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.997

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UNC79	NM_001395159.1	c.7804-160C>A		intron_variant		ENST00000695012.1	NP_001382088.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UNC79	ENST00000695012.1	c.7804-160C>A		intron_variant			NM_001395159.1	ENSP00000511643.1

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108264 AN: 151962 Hom.: 39153 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.713 AC: 108367 AN: 152080 Hom.: 39196 Cov.: 32 AF XY: 0.710 AC XY: 52761 AN XY: 74344

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.718

Alfa AF: 0.699 Hom.: 21250

Bravo AF: 0.718

Asia WGS AF: 0.496 AC: 1730 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.23
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs943323; hg19: chr14-94160521;