rs1167796

chr7-75543861-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.2766+834C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,046 control chromosomes in the GnomAD database, including 9,624 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 0.33 (9624 hom., cov: 31)
• Consequence: HIP1 NM_005338.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

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 (Cadd=0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HIP1	NM_005338.7	c.2766+834C>T		intron_variant		ENST00000336926.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HIP1	ENST00000336926.11	c.2766+834C>T		intron_variant		1	NM_005338.7	P1
HIP1	ENST00000616821.4	c.2679+834C>T		intron_variant		1
HIP1	ENST00000434438.6	c.2613+834C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49721 AN: 151928 Hom.: 9632 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.327 AC: 49710 AN: 152046 Hom.: 9624 Cov.: 31 AF XY: 0.330 AC XY: 24518 AN XY: 74308

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.343

Alfa AF: 0.405 Hom.: 25802

Bravo AF: 0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Cadd	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1167796; hg19: -;