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GeneBe

rs17721701

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022475.3(HHIP):c.832-8964T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,782 control chromosomes in the GnomAD database, including 20,257 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 0.50 ( 20257 hom., cov: 32)

Consequence

HHIP
NM_022475.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.970
Variant links:
Genes affected
HHIP (HGNC:14866): (hedgehog interacting protein) This gene encodes a member of the hedgehog-interacting protein (HHIP) family. The hedgehog (HH) proteins are evolutionarily conserved protein, which are important morphogens for a wide range of developmental processes, including anteroposterior patterns of limbs and regulation of left-right asymmetry in embryonic development. Multiple cell-surface receptors are responsible for transducing and/or regulating HH signals. The HHIP encoded by this gene is a highly conserved, vertebrate-specific inhibitor of HH signaling. It interacts with all three HH family members, SHH, IHH and DHH. Two single nucleotide polymorphisms (SNPs) near this gene are significantly associated with risk of chronic obstructive pulmonary disease (COPD). A single nucleotide polymorphism in this gene is also strongly associated with human height.[provided by RefSeq, Feb 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HHIPNM_022475.3 linkuse as main transcriptc.832-8964T>C intron_variant ENST00000296575.8
LOC124900791XR_007058289.1 linkuse as main transcriptn.8698A>G non_coding_transcript_exon_variant 2/2
HHIPXM_005263178.6 linkuse as main transcriptc.832-8964T>C intron_variant
HHIPXM_006714288.5 linkuse as main transcriptc.832-8964T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HHIPENST00000296575.8 linkuse as main transcriptc.832-8964T>C intron_variant 1 NM_022475.3 P1Q96QV1-1

Frequencies

GnomAD3 genomes
AF:
0.502
AC:
76205
AN:
151664
Hom.:
20229
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.322
Gnomad AMI
AF:
0.537
Gnomad AMR
AF:
0.557
Gnomad ASJ
AF:
0.568
Gnomad EAS
AF:
0.425
Gnomad SAS
AF:
0.769
Gnomad FIN
AF:
0.587
Gnomad MID
AF:
0.506
Gnomad NFE
AF:
0.571
Gnomad OTH
AF:
0.487
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.503
AC:
76271
AN:
151782
Hom.:
20257
Cov.:
32
AF XY:
0.507
AC XY:
37571
AN XY:
74164
show subpopulations
Gnomad4 AFR
AF:
0.322
Gnomad4 AMR
AF:
0.558
Gnomad4 ASJ
AF:
0.568
Gnomad4 EAS
AF:
0.425
Gnomad4 SAS
AF:
0.770
Gnomad4 FIN
AF:
0.587
Gnomad4 NFE
AF:
0.571
Gnomad4 OTH
AF:
0.488
Alfa
AF:
0.562
Hom.:
13933
Bravo
AF:
0.486
Asia WGS
AF:
0.582
AC:
2018
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
0.54
Dann
Benign
0.58

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17721701; hg19: chr4-145618719; API