rs13384791

Variant summary

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

The NM_001321623.1(HYCC2):​c.-128-848T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 151,982 control chromosomes in the GnomAD database, including 4,465 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 0.22 ( 4465 hom., cov: 31)

Consequence

HYCC2
NM_001321623.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.46
Variant links:
Genes affected
HYCC2 (HGNC:28593): (hyccin PI4KA lipid kinase complex subunit 2) Predicted to be involved in phosphatidylinositol phosphate biosynthetic process and protein localization to plasma membrane. Predicted to be located in cytosol. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HYCC2NM_001321623.1 linkuse as main transcriptc.-128-848T>C intron_variant ENST00000681958.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HYCC2ENST00000681958.1 linkuse as main transcriptc.-128-848T>C intron_variant NM_001321623.1 P3

Frequencies

GnomAD3 genomes
AF:
0.217
AC:
33025
AN:
151864
Hom.:
4458
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.376
Gnomad AMI
AF:
0.137
Gnomad AMR
AF:
0.165
Gnomad ASJ
AF:
0.215
Gnomad EAS
AF:
0.00827
Gnomad SAS
AF:
0.0712
Gnomad FIN
AF:
0.165
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.170
Gnomad OTH
AF:
0.208
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.218
AC:
33068
AN:
151982
Hom.:
4465
Cov.:
31
AF XY:
0.213
AC XY:
15850
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.376
Gnomad4 AMR
AF:
0.165
Gnomad4 ASJ
AF:
0.215
Gnomad4 EAS
AF:
0.00829
Gnomad4 SAS
AF:
0.0713
Gnomad4 FIN
AF:
0.165
Gnomad4 NFE
AF:
0.170
Gnomad4 OTH
AF:
0.206
Alfa
AF:
0.211
Hom.:
652
Bravo
AF:
0.227
Asia WGS
AF:
0.0670
AC:
235
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
3.8
DANN
Benign
0.56

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: rs13384791; hg19: chr2-201911164; API