rs235987

Variant summary

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

The NM_001270974.2(HYDIN):​c.-24+15119G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,118 control chromosomes in the GnomAD database, including 2,929 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 0.17 ( 2929 hom., cov: 31)

Consequence

HYDIN
NM_001270974.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.332
Variant links:
Genes affected
HYDIN (HGNC:19368): (HYDIN axonemal central pair apparatus protein) This gene encodes a protein that may be involved in cilia motility. Mutations in this gene cause of autosomal recessive primary ciliary dyskinesia-5, a disorder characterized by the accumulation of cerebrospinal fluid within the ventricles of the brain. A duplicate copy of this gene has been found in humans on chromosome 1. [provided by RefSeq, Jan 2013]

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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=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HYDINNM_001270974.2 linkuse as main transcriptc.-24+15119G>A intron_variant ENST00000393567.7
HYDINNM_001198542.1 linkuse as main transcriptc.58+15187G>A intron_variant
HYDINNM_001198543.1 linkuse as main transcriptc.28+15217G>A intron_variant
HYDINNM_017558.5 linkuse as main transcriptc.-24+15119G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HYDINENST00000393567.7 linkuse as main transcriptc.-24+15119G>A intron_variant 5 NM_001270974.2 P1Q4G0P3-1

Frequencies

GnomAD3 genomes
AF:
0.173
AC:
26222
AN:
152000
Hom.:
2932
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0428
Gnomad AMI
AF:
0.291
Gnomad AMR
AF:
0.163
Gnomad ASJ
AF:
0.313
Gnomad EAS
AF:
0.0457
Gnomad SAS
AF:
0.233
Gnomad FIN
AF:
0.257
Gnomad MID
AF:
0.364
Gnomad NFE
AF:
0.235
Gnomad OTH
AF:
0.212
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.172
AC:
26214
AN:
152118
Hom.:
2929
Cov.:
31
AF XY:
0.175
AC XY:
13010
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.0427
Gnomad4 AMR
AF:
0.163
Gnomad4 ASJ
AF:
0.313
Gnomad4 EAS
AF:
0.0458
Gnomad4 SAS
AF:
0.233
Gnomad4 FIN
AF:
0.257
Gnomad4 NFE
AF:
0.235
Gnomad4 OTH
AF:
0.211
Alfa
AF:
0.232
Hom.:
8705
Bravo
AF:
0.161
Asia WGS
AF:
0.122
AC:
425
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
8.2
DANN
Benign
0.80

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: rs235987; hg19: chr16-71249346; API