chr10-100315722-G-A

Variant names:

• chr10-100315722-G-A
• rs603424
• NM_016112.3:c.349+13489C>T

Variant summary

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

The NM_016112.3(PKD2L1):​c.349+13489C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,012 control chromosomes in the GnomAD database, including 12,219 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 0.33 (12219 hom., cov: 32)
• Consequence: PKD2L1 NM_016112.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 98 publications found

Genes affected

PKD2L1 (HGNC:9011): (polycystin 2 like 1, transient receptor potential cation channel) This gene encodes a member of the polycystin protein family. The encoded protein contains multiple transmembrane domains, and cytoplasmic N- and C-termini. The protein may be an integral membrane protein involved in cell-cell/matrix interactions. This protein functions as a calcium-regulated nonselective cation channel. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.667 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016112.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKD2L1	NM_016112.3	MANE Select	c.349+13489C>T		intron	N/A	NP_057196.2
	PKD2L1	NM_001253837.2		c.208+13489C>T		intron	N/A	NP_001240766.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKD2L1	ENST00000318222.4	TSL:1 MANE Select	c.349+13489C>T		intron	N/A	ENSP00000325296.3
	PKD2L1	ENST00000528248.1	TSL:1	n.*89+13489C>T		intron	N/A	ENSP00000436514.1
	PKD2L1	ENST00000465680.2	TSL:3	c.103+14147C>T		intron	N/A	ENSP00000434019.1

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49945 AN: 151894 Hom.: 12177 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.0702

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.329 AC: 50041 AN: 152012 Hom.: 12219 Cov.: 32 AF XY: 0.325 AC XY: 24154 AN XY: 74314

African (AFR) AF: 0.674 AC: 27908 AN: 41430

American (AMR) AF: 0.224 AC: 3428 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1173 AN: 3470

East Asian (EAS) AF: 0.0702 AC: 364 AN: 5188

South Asian (SAS) AF: 0.452 AC: 2177 AN: 4814

European-Finnish (FIN) AF: 0.113 AC: 1199 AN: 10572

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

European-Non Finnish (NFE) AF: 0.186 AC: 12643 AN: 67942

Other (OTH) AF: 0.342 AC: 722 AN: 2112

Alfa AF: 0.233 Hom.: 26164

Bravo AF: 0.347

Asia WGS AF: 0.331 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.77
PhyloP100		-0.64
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: rs603424; hg19: chr10-102075479;