chr9-5335590-T-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_006911.4(RLN1):āc.219A>Cā(p.Val73=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00834 in 1,596,512 control chromosomes in the GnomAD database, including 155 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0074 ( 23 hom., cov: 32)
Exomes š: 0.0084 ( 132 hom. )
Consequence
RLN1
NM_006911.4 synonymous
NM_006911.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.264
Genes affected
RLN1 (HGNC:10026): (relaxin 1) Relaxins are known endocrine and autocrine/paracrine hormones, belonging to the insulin gene superfamily. In humans there are three non-allelic relaxin genes, RLN1, RLN2 and RLN3, where RLN1 and RLN2 share high sequence homology. The protein encoded by this gene is synthesized as a single-chain polypeptide but the active form consists of an A chain and a B chain linked by disulfide bonds. Relaxin is produced by the ovary, and targets the mammalian reproductive system to ripen the cervix, elongate the pubic symphysis and inhibit uterine contraction. It may have additional roles in enhancing sperm motility, regulating blood pressure, controlling heart rate and releasing oxytocin and vasopressin. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
Variant 9-5335590-T-G is Benign according to our data. Variant chr9-5335590-T-G is described in ClinVar as [Benign]. Clinvar id is 718077.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.264 with no splicing effect.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00845 (12201/1444532) while in subpopulation MID AF= 0.0253 (144/5692). AF 95% confidence interval is 0.0219. There are 132 homozygotes in gnomad4_exome. There are 6289 alleles in male gnomad4_exome subpopulation. Median coverage is 29. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 23 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RLN1 | NM_006911.4 | c.219A>C | p.Val73= | synonymous_variant | 2/2 | ENST00000223862.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RLN1 | ENST00000223862.2 | c.219A>C | p.Val73= | synonymous_variant | 2/2 | 1 | NM_006911.4 | P1 | |
RLN1 | ENST00000487557.2 | n.143A>C | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00737 AC: 1119AN: 151864Hom.: 23 Cov.: 32
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GnomAD3 exomes AF: 0.00855 AC: 2082AN: 243530Hom.: 34 AF XY: 0.00918 AC XY: 1208AN XY: 131656
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GnomAD4 exome AF: 0.00845 AC: 12201AN: 1444532Hom.: 132 Cov.: 29 AF XY: 0.00875 AC XY: 6289AN XY: 718532
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GnomAD4 genome AF: 0.00737 AC: 1120AN: 151980Hom.: 23 Cov.: 32 AF XY: 0.00748 AC XY: 556AN XY: 74286
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 13, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at