rs7800244

Variant names:

• chr7-47740371-G-T
• rs7800244
• ENST00000648482.1:c.*393C>A

Variant summary

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

The ENST00000648482.1(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 ENST00000648482.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 6 publications found

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]

PKD1L1 Gene-Disease associations (from GenCC):

• heterotaxy, visceral, 8, autosomal

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
• situs inversus

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648482.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKD1L1	ENST00000648482.1		c.*393C>A		3_prime_UTR	Exon 8 of 8	ENSP00000496786.1	A0A3B3IRH7

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

African (AFR) AF: 0.0801 AC: 3316 AN: 41396

American (AMR) AF: 0.161 AC: 2451 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3470

East Asian (EAS) AF: 0.188 AC: 973 AN: 5178

South Asian (SAS) AF: 0.172 AC: 825 AN: 4808

European-Finnish (FIN) AF: 0.218 AC: 2290 AN: 10508

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.178 AC: 12084 AN: 67956

Other (OTH) AF: 0.144 AC: 304 AN: 2108

Alfa AF: 0.165 Hom.: 6931

Bravo AF: 0.143

Asia WGS AF: 0.177 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.40
PhyloP100		0.50

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7800244;

hg19: chr7-47779969;