chr2-195926552-T-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_018897.3(DNAH7):āc.3486A>Cā(p.Ala1162=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 1,591,136 control chromosomes in the GnomAD database, including 314,517 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.50 ( 22192 hom., cov: 31)
Exomes š: 0.63 ( 292325 hom. )
Consequence
DNAH7
NM_018897.3 synonymous
NM_018897.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.184
Genes affected
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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=-0.83).
BP6
Variant 2-195926552-T-G is Benign according to our data. Variant chr2-195926552-T-G is described in ClinVar as [Benign]. Clinvar id is 402753.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.184 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH7 | NM_018897.3 | c.3486A>C | p.Ala1162= | synonymous_variant | 22/65 | ENST00000312428.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH7 | ENST00000312428.11 | c.3486A>C | p.Ala1162= | synonymous_variant | 22/65 | 1 | NM_018897.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.499 AC: 75818AN: 151808Hom.: 22189 Cov.: 31
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GnomAD3 exomes AF: 0.597 AC: 137100AN: 229746Hom.: 42857 AF XY: 0.605 AC XY: 75753AN XY: 125300
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GnomAD4 exome AF: 0.631 AC: 908071AN: 1439210Hom.: 292325 Cov.: 38 AF XY: 0.632 AC XY: 452432AN XY: 715978
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GnomAD4 genome AF: 0.499 AC: 75827AN: 151926Hom.: 22192 Cov.: 31 AF XY: 0.502 AC XY: 37289AN XY: 74244
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at