chr7-47740371-G-T

Variant names:

• chr7-47740371-G-T
• rs7800244
• ENST00000648482:c.*393C>A

Variant summary

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

The ENST00000648482(PKD1L1):​c.*393C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 151,898 control chromosomes in the GnomAD database, including 1,968 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 0.15 (1968 hom., cov: 32)
• Consequence: PKD1L1 ENST00000648482 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

Genes affected

PKD1L1 (HGNC:18053): (polycystin 1 like 1, transient receptor potential channel interacting) This gene encodes a member of the polycystin protein family containing 11 transmembrane domains, a receptor for egg jelly (REJ) domain, and a polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain. The encoded protein may play a role in the male reproductive system. Alternative splice variants have been described but their biological nature has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PKD1L1	ENST00000648482	c.*393C>A		3_prime_UTR_variant	Exon 8 of 8			ENSP00000496786.1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22865 AN: 151788 Hom.: 1967 Cov.: 32

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.151 AC: 22872 AN: 151898 Hom.: 1968 Cov.: 32 AF XY: 0.154 AC XY: 11396 AN XY: 74238

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.144

Alfa AF: 0.171 Hom.: 3087

Bravo AF: 0.143

Asia WGS AF: 0.177 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7800244; hg19: chr7-47779969;