rs7151505

Variant names:

• chr14-93534596-G-A
• rs7151505
• NM_001395159.1:c.1122+2018G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-93534596-G-A
• chr14-93534596-G-C

Variant summary

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

The NM_001395159.1(UNC79):​c.1122+2018G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,868 control chromosomes in the GnomAD database, including 23,145 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 0.55 (23145 hom., cov: 31)
• Consequence: UNC79 NM_001395159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 6 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UNC79	NM_001395159.1	c.1122+2018G>A		intron_variant	Intron 11 of 51	ENST00000695012.1	NP_001382088.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UNC79	ENST00000695012.1	c.1122+2018G>A		intron_variant	Intron 11 of 51		NM_001395159.1	ENSP00000511643.1

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83305 AN: 151750 Hom.: 23140 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.549 AC: 83354 AN: 151868 Hom.: 23145 Cov.: 31 AF XY: 0.550 AC XY: 40800 AN XY: 74230

African (AFR) AF: 0.530 AC: 21923 AN: 41382

American (AMR) AF: 0.634 AC: 9675 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1757 AN: 3468

East Asian (EAS) AF: 0.279 AC: 1436 AN: 5146

South Asian (SAS) AF: 0.451 AC: 2175 AN: 4824

European-Finnish (FIN) AF: 0.550 AC: 5799 AN: 10546

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38724 AN: 67924

Other (OTH) AF: 0.573 AC: 1209 AN: 2110

Alfa AF: 0.565 Hom.: 30302

Bravo AF: 0.553

Asia WGS AF: 0.378 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.81
DANN	Benign	0.56
PhyloP100		-0.20
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: rs7151505; hg19: chr14-94000942;