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GeneBe

rs2672589

Variant summary

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

The NM_002775.5(HTRA1):c.472+13348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,250 control chromosomes in the GnomAD database, including 31,799 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 0.64 ( 31799 hom., cov: 35)

Consequence

HTRA1
NM_002775.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.617
Variant links:
Genes affected
HTRA1 (HGNC:9476): (HtrA serine peptidase 1) This gene encodes a member of the trypsin family of serine proteases. This protein is a secreted enzyme that is proposed to regulate the availability of insulin-like growth factors (IGFs) by cleaving IGF-binding proteins. It has also been suggested to be a regulator of cell growth. Variations in the promoter region of this gene are the cause of susceptibility to age-related macular degeneration type 7. [provided by RefSeq, Jul 2008]

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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 (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HTRA1NM_002775.5 linkuse as main transcriptc.472+13348G>A intron_variant ENST00000368984.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HTRA1ENST00000368984.8 linkuse as main transcriptc.472+13348G>A intron_variant 1 NM_002775.5 P1
HTRA1ENST00000648167.1 linkuse as main transcriptc.155-13430G>A intron_variant

Frequencies

GnomAD3 genomes
AF:
0.643
AC:
97823
AN:
152132
Hom.:
31756
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.729
Gnomad AMI
AF:
0.670
Gnomad AMR
AF:
0.568
Gnomad ASJ
AF:
0.602
Gnomad EAS
AF:
0.761
Gnomad SAS
AF:
0.624
Gnomad FIN
AF:
0.576
Gnomad MID
AF:
0.541
Gnomad NFE
AF:
0.613
Gnomad OTH
AF:
0.633
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.643
AC:
97927
AN:
152250
Hom.:
31799
Cov.:
35
AF XY:
0.641
AC XY:
47681
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.730
Gnomad4 AMR
AF:
0.568
Gnomad4 ASJ
AF:
0.602
Gnomad4 EAS
AF:
0.762
Gnomad4 SAS
AF:
0.623
Gnomad4 FIN
AF:
0.576
Gnomad4 NFE
AF:
0.613
Gnomad4 OTH
AF:
0.630
Alfa
AF:
0.629
Hom.:
42869
Bravo
AF:
0.644
Asia WGS
AF:
0.699
AC:
2427
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
2.4
Dann
Benign
0.46

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: rs2672589; hg19: chr10-124234988; API