chr7-37850714-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_016616.5(NME8):c.177C>T(p.Asp59Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 1,605,020 control chromosomes in the GnomAD database, including 49,984 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_016616.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NME8 | ENST00000199447.9 | c.177C>T | p.Asp59Asp | synonymous_variant | Exon 5 of 18 | 1 | NM_016616.5 | ENSP00000199447.4 | ||
ENSG00000290149 | ENST00000476620.1 | c.-109-6560C>T | intron_variant | Intron 1 of 3 | 4 | ENSP00000425858.1 |
Frequencies
GnomAD3 genomes AF: 0.275 AC: 41818AN: 151936Hom.: 6003 Cov.: 33
GnomAD3 exomes AF: 0.229 AC: 57476AN: 250792Hom.: 7102 AF XY: 0.224 AC XY: 30324AN XY: 135520
GnomAD4 exome AF: 0.241 AC: 349803AN: 1452966Hom.: 43970 Cov.: 31 AF XY: 0.238 AC XY: 172214AN XY: 723382
GnomAD4 genome AF: 0.275 AC: 41860AN: 152054Hom.: 6014 Cov.: 33 AF XY: 0.272 AC XY: 20220AN XY: 74332
ClinVar
Submissions by phenotype
not specified Benign:2
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Asp59Asp in exon 5 of TXNDC3: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. It has been identified in 36.8% (1622/4406) of African American chromosomes from a broad population by the NHLBI Exome Sequenc ing Project (http://evs.gs.washington.edu/EVS; dbSNP rs2598044). -
Primary ciliary dyskinesia 6 Benign:2
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Primary ciliary dyskinesia Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at