rs1167827

chr7-75533848-G-A

Variant summary

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

The NM_005338.7(HIP1):c.*4324C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 235,176 control chromosomes in the GnomAD database, including 25,500 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 0.38 (13949 hom., cov: 32)
  • Exomes 𝑓: 0.48 (11551 hom.)
• Consequence: HIP1 NM_005338.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

Genes affected

HIP1 (HGNC:4913): (huntingtin interacting protein 1) The product of this gene is a membrane-associated protein that functions in clathrin-mediated endocytosis and protein trafficking within the cell. The encoded protein binds to the huntingtin protein in the brain; this interaction is lost in Huntington's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HIP1	NM_005338.7	c.*4324C>T		3_prime_UTR_variant	31/31	ENST00000336926.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HIP1	ENST00000336926.11	c.*4324C>T		3_prime_UTR_variant	31/31	1	NM_005338.7	P1

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57891 AN: 152026 Hom.: 13934 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.398

GnomAD4 exome AF: 0.485 AC: 40263 AN: 83030 Hom.: 11551 Cov.: 0 AF XY: 0.483 AC XY: 18538 AN XY: 38420

Gnomad4 AFR exome AF: 0.114

Gnomad4 AMR exome AF: 0.569

Gnomad4 ASJ exome AF: 0.390

Gnomad4 EAS exome AF: 0.968

Gnomad4 SAS exome AF: 0.497

Gnomad4 FIN exome AF: 0.588

Gnomad4 NFE exome AF: 0.419

Gnomad4 OTH exome AF: 0.415

GnomAD4 genome AF: 0.381 AC: 57923 AN: 152146 Hom.: 13949 Cov.: 32 AF XY: 0.394 AC XY: 29309 AN XY: 74364

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.402

Alfa AF: 0.428 Hom.: 26442

Bravo AF: 0.370

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.8

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1167827; hg19: chr7-75163169;