rs5876252

Variant names:

• chr6-52066088-TAAAA-T
• rs5876252
• NM_138694.4:c.779-15_779-12delTTTT

Your query was ambiguous. Multiple possible variants found:

• chr6-52066088-TAAAA-T
• chr6-52066088-TAAAA-TA
• chr6-52066088-TAAAA-TAA
• chr6-52066088-TAAAA-TAAA
• chr6-52066088-TAAAA-TAAAAA
• chr6-52066088-TAAAA-TAAAAAA
• chr6-52066088-TAAAA-TAAAAAAA
• chr6-52066088-TAAAA-TAAAAAAAA
• chr6-52066088-TAAAA-TAAAAAAAAA
• chr6-52066088-TAAAA-TAAAAAAAAAA
• chr6-52066088-TAAAA-TAAAAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000371117.8(PKHD1):​c.779-15_779-12delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000123 in 815,302 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.000012 (0 hom.)
• Consequence: PKHD1 ENST00000371117.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639
• Publications: 0 publications found

Genes affected

PKHD1 (HGNC:9016): (PKHD1 ciliary IPT domain containing fibrocystin/polyductin) The protein encoded by this gene is predicted to have a single transmembrane (TM)-spanning domain and multiple copies of an immunoglobulin-like plexin-transcription-factor domain. Alternative splicing results in two transcript variants encoding different isoforms. Other alternatively spliced transcripts have been described, but the full length sequences have not been determined. Several of these transcripts are predicted to encode truncated products which lack the TM and may be secreted. Mutations in this gene cause autosomal recessive polycystic kidney disease, also known as polycystic kidney and hepatic disease-1. [provided by RefSeq, Jul 2008]

PKHD1 Gene-Disease associations (from GenCC):

• autosomal recessive polycystic kidney disease

  Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Myriad Women’s Health, Orphanet
• polycystic kidney disease 4

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Laboratory for Molecular Medicine, Genomics England PanelApp
• Caroli disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000371117.8. 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
	PKHD1	NM_138694.4	MANE Select	c.779-15_779-12delTTTT		intron	N/A	NP_619639.3
	PKHD1	NM_170724.3		c.779-15_779-12delTTTT		intron	N/A	NP_733842.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKHD1	ENST00000371117.8	TSL:1 MANE Select	c.779-15_779-12delTTTT		intron	N/A	ENSP00000360158.3
	PKHD1	ENST00000340994.4	TSL:5	c.779-15_779-12delTTTT		intron	N/A	ENSP00000341097.4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.0000123 AC: 10 AN: 815302 Hom.: 0 AF XY: 0.0000163 AC XY: 7 AN XY: 428416

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000945 AC: 2 AN: 21156

American (AMR) AF: 0.00 AC: 0 AN: 38640

Ashkenazi Jewish (ASJ) AF: 0.0000475 AC: 1 AN: 21064

East Asian (EAS) AF: 0.00 AC: 0 AN: 33812

South Asian (SAS) AF: 0.00 AC: 0 AN: 67686

European-Finnish (FIN) AF: 0.0000238 AC: 1 AN: 42092

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4138

European-Non Finnish (NFE) AF: 0.0000109 AC: 6 AN: 548474

Other (OTH) AF: 0.00 AC: 0 AN: 38240

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.24		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.24		Position offset: -32

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

Other links and lift over

dbSNP: rs5876252; hg19: chr6-51930886;