19-917520-G-A

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_032551.5(KISS1R):​c.18G>A​(p.Thr6Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00038 in 1,501,158 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.00038 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00038 ( 2 hom. )

Consequence

KISS1R
NM_032551.5 synonymous

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.29
Variant links:
Genes affected
KISS1R (HGNC:4510): (KISS1 receptor) The protein encoded by this gene is a galanin-like G protein-coupled receptor that binds metastin, a peptide encoded by the metastasis suppressor gene KISS1. The tissue distribution of the expressed gene suggests that it is involved in the regulation of endocrine function, and this is supported by the finding that this gene appears to play a role in the onset of puberty. Mutations in this gene have been associated with hypogonadotropic hypogonadism and central precocious puberty. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 19-917520-G-A is Benign according to our data. Variant chr19-917520-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1590131.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-2.3 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KISS1RNM_032551.5 linkc.18G>A p.Thr6Thr synonymous_variant 1/5 ENST00000234371.10 NP_115940.2 Q969F8
KISS1RXM_047439545.1 linkc.18G>A p.Thr6Thr synonymous_variant 1/4 XP_047295501.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KISS1RENST00000234371.10 linkc.18G>A p.Thr6Thr synonymous_variant 1/51 NM_032551.5 ENSP00000234371.3 Q969F8
KISS1RENST00000606939.2 linkc.18G>A p.Thr6Thr synonymous_variant 1/45 ENSP00000475639.1 U3KQ86
KISS1RENST00000592648.1 linkc.18G>A p.Thr6Thr synonymous_variant 1/25 ENSP00000467666.1 K7EQ45

Frequencies

GnomAD3 genomes
AF:
0.000381
AC:
58
AN:
152192
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.0127
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000132
Gnomad OTH
AF:
0.000955
GnomAD3 exomes
AF:
0.00105
AC:
112
AN:
106278
Hom.:
0
AF XY:
0.00116
AC XY:
68
AN XY:
58484
show subpopulations
Gnomad AFR exome
AF:
0.000277
Gnomad AMR exome
AF:
0.0000976
Gnomad ASJ exome
AF:
0.0163
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000242
Gnomad OTH exome
AF:
0.000600
GnomAD4 exome
AF:
0.000380
AC:
512
AN:
1348966
Hom.:
2
Cov.:
30
AF XY:
0.000406
AC XY:
269
AN XY:
663346
show subpopulations
Gnomad4 AFR exome
AF:
0.0000354
Gnomad4 AMR exome
AF:
0.0000948
Gnomad4 ASJ exome
AF:
0.0159
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000734
Gnomad4 OTH exome
AF:
0.00114
GnomAD4 genome
AF:
0.000381
AC:
58
AN:
152192
Hom.:
0
Cov.:
33
AF XY:
0.000390
AC XY:
29
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.0127
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000132
Gnomad4 OTH
AF:
0.000955
Alfa
AF:
0.00240
Hom.:
1
Bravo
AF:
0.000495

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

KISS1R-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesJun 28, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpApr 10, 2023- -
Hypogonadotropic hypogonadism 8 with or without anosmia;C3805879:Central precocious puberty 1 Benign:1
Likely benign, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsJan 14, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
1.3
DANN
Benign
0.83
RBP_binding_hub_radar
1.1
RBP_regulation_power_radar
2.3

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: rs755924784; hg19: chr19-917520; API