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GeneBe

rs11200638

Variant summary

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

The ENST00000650300.1(null):n.356C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,162 control chromosomes in the GnomAD database, including 4,399 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

Frequency

Genomes: 𝑓 0.23 ( 4399 hom., cov: 34)

Consequence


ENST00000650300.1 non_coding_transcript_exon

Scores

2

Clinical Significance

risk factor no assertion criteria provided O:2

Conservation

PhyloP100: -0.125
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=-0.8).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105378525XR_946382.3 linkuse as main transcriptn.378C>T non_coding_transcript_exon_variant 1/3
LOC105378525XR_946383.3 linkuse as main transcriptn.356C>T non_coding_transcript_exon_variant 1/4
LOC105378525XR_946384.3 linkuse as main transcriptn.356C>T non_coding_transcript_exon_variant 1/4
LOC105378525XR_946385.3 linkuse as main transcriptn.356C>T non_coding_transcript_exon_variant 1/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000650300.1 linkuse as main transcriptn.356C>T non_coding_transcript_exon_variant 1/3
HTRA1ENST00000648167.1 linkuse as main transcriptc.154+2319G>A intron_variant

Frequencies

GnomAD3 genomes
AF:
0.234
AC:
35620
AN:
152042
Hom.:
4389
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.234
Gnomad AMI
AF:
0.237
Gnomad AMR
AF:
0.229
Gnomad ASJ
AF:
0.208
Gnomad EAS
AF:
0.424
Gnomad SAS
AF:
0.315
Gnomad FIN
AF:
0.235
Gnomad MID
AF:
0.191
Gnomad NFE
AF:
0.217
Gnomad OTH
AF:
0.238
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.234
AC:
35666
AN:
152162
Hom.:
4399
Cov.:
34
AF XY:
0.237
AC XY:
17634
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.234
Gnomad4 AMR
AF:
0.230
Gnomad4 ASJ
AF:
0.208
Gnomad4 EAS
AF:
0.424
Gnomad4 SAS
AF:
0.316
Gnomad4 FIN
AF:
0.235
Gnomad4 NFE
AF:
0.217
Gnomad4 OTH
AF:
0.235
Alfa
AF:
0.213
Hom.:
2603
Bravo
AF:
0.236
Asia WGS
AF:
0.369
AC:
1277
AN:
3478

ClinVar

Significance: risk factor
Submissions summary: Other:2
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Age related macular degeneration 7 Other:1
risk factor, no assertion criteria providedliterature onlyOMIMFeb 18, 2015- -
Susceptibility to neovascular type of age-related macular degeneration Other:1
risk factor, no assertion criteria providedliterature onlyOMIMFeb 18, 2015- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
Cadd
Benign
6.4
Dann
Benign
0.87

Splicing

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: rs11200638; hg19: chr10-124220544; COSMIC: COSV64564929; API