rs1167796

Variant names:

• chr7-75543861-G-A
• rs1167796
• NM_005338.7:c.2766+834C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 43 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HIP1	NM_005338.7	c.2766+834C>T		intron_variant	Intron 27 of 30	ENST00000336926.11	NP_005329.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HIP1	ENST00000336926.11	c.2766+834C>T		intron_variant	Intron 27 of 30	1	NM_005338.7	ENSP00000336747.6
HIP1	ENST00000616821.4	c.2679+834C>T		intron_variant	Intron 27 of 30	1		ENSP00000484528.1
HIP1	ENST00000434438.6	c.2613+834C>T		intron_variant	Intron 25 of 28	2		ENSP00000410300.2

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

African (AFR) AF: 0.110 AC: 4581 AN: 41518

American (AMR) AF: 0.325 AC: 4955 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1374 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1560 AN: 5152

South Asian (SAS) AF: 0.394 AC: 1898 AN: 4822

European-Finnish (FIN) AF: 0.486 AC: 5131 AN: 10556

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28841 AN: 67958

Other (OTH) AF: 0.343 AC: 724 AN: 2110

Alfa AF: 0.392 Hom.: 55495

Bravo AF: 0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.77
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1167796; hg19: -;