chr10-100306428-C-T

Variant names:

• chr10-100306428-C-T
• rs17112901
• NM_016112.3:c.350-6710G>A

Variant summary

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

The NM_016112.3(PKD2L1):​c.350-6710G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,110 control chromosomes in the GnomAD database, including 2,659 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 0.17 (2659 hom., cov: 31)
• Consequence: PKD2L1 NM_016112.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 7 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKD2L1	NM_016112.3	MANE Select	c.350-6710G>A		intron	N/A	NP_057196.2
	PKD2L1	NM_001253837.2		c.209-6710G>A		intron	N/A	NP_001240766.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKD2L1	ENST00000318222.4	TSL:1 MANE Select	c.350-6710G>A		intron	N/A	ENSP00000325296.3	Q9P0L9-1
	PKD2L1	ENST00000528248.1	TSL:1	n.*90-6710G>A		intron	N/A	ENSP00000436514.1	H0YET4
	PKD2L1	ENST00000465680.2	TSL:3	c.104-17950G>A		intron	N/A	ENSP00000434019.1	H0YDN7

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26027 AN: 151988 Hom.: 2657 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.171 AC: 26062 AN: 152110 Hom.: 2659 Cov.: 31 AF XY: 0.171 AC XY: 12734 AN XY: 74382

African (AFR) AF: 0.288 AC: 11941 AN: 41468

American (AMR) AF: 0.165 AC: 2519 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3464

East Asian (EAS) AF: 0.119 AC: 616 AN: 5168

South Asian (SAS) AF: 0.140 AC: 675 AN: 4824

European-Finnish (FIN) AF: 0.155 AC: 1640 AN: 10598

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7884 AN: 67982

Other (OTH) AF: 0.152 AC: 322 AN: 2112

Alfa AF: 0.145 Hom.: 3203

Bravo AF: 0.175

Asia WGS AF: 0.177 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.35
PhyloP100		-0.41
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: rs17112901; hg19: chr10-102066185;