NM_181536.2:c.4926+1598A>G

Variant names:

• chr16-71931822-T-C
• rs952160
• NM_181536.2:c.4926+1598A>G

Variant summary

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

The NM_181536.2(PKD1L3):​c.4926+1598A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,982 control chromosomes in the GnomAD database, including 9,344 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 0.34 (9344 hom., cov: 31)
• Consequence: PKD1L3 NM_181536.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 4 publications found

Genes affected

PKD1L3 (HGNC:21716): (polycystin 1 like 3, transient receptor potential channel interacting) This gene encodes a member of the polycystin protein family. The encoded protein contains 11 transmembrane domains, a latrophilin/CL-1-like GPCR proteolytic site (GPS) domain, and a polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain. This protein may function as a component of cation channel pores.[provided by RefSeq, Apr 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PKD1L3	NM_181536.2	c.4926+1598A>G		intron_variant	Intron 28 of 29	ENST00000620267.2	NP_853514.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PKD1L3	ENST00000620267.2	c.4926+1598A>G		intron_variant	Intron 28 of 29	1	NM_181536.2	ENSP00000480090.1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51496 AN: 151862 Hom.: 9342 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.339 AC: 51515 AN: 151982 Hom.: 9344 Cov.: 31 AF XY: 0.342 AC XY: 25435 AN XY: 74294

African (AFR) AF: 0.277 AC: 11474 AN: 41448

American (AMR) AF: 0.453 AC: 6918 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3472

East Asian (EAS) AF: 0.660 AC: 3401 AN: 5154

South Asian (SAS) AF: 0.313 AC: 1508 AN: 4814

European-Finnish (FIN) AF: 0.357 AC: 3768 AN: 10550

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22299 AN: 67962

Other (OTH) AF: 0.314 AC: 661 AN: 2108

Alfa AF: 0.332 Hom.: 7273

Bravo AF: 0.349

Asia WGS AF: 0.455 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.43
PhyloP100		0.31

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: rs952160; hg19: chr16-71965725;