10-68431874-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001080449.3(DNA2):c.1971G>A(p.Thr657Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.045 in 1,608,528 control chromosomes in the GnomAD database, including 2,012 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001080449.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNA2 | ENST00000358410.8 | c.1971G>A | p.Thr657Thr | synonymous_variant | Exon 13 of 21 | 1 | NM_001080449.3 | ENSP00000351185.3 | ||
DNA2 | ENST00000551118.6 | c.1971G>A | p.Thr657Thr | synonymous_variant | Exon 13 of 17 | 5 | ENSP00000450393.3 | |||
DNA2 | ENST00000399179.6 | n.1971G>A | non_coding_transcript_exon_variant | Exon 14 of 22 | 2 | ENSP00000382132.3 |
Frequencies
GnomAD3 genomes AF: 0.0376 AC: 5724AN: 152118Hom.: 155 Cov.: 32
GnomAD3 exomes AF: 0.0451 AC: 11189AN: 247872Hom.: 390 AF XY: 0.0470 AC XY: 6323AN XY: 134462
GnomAD4 exome AF: 0.0457 AC: 66586AN: 1456292Hom.: 1858 Cov.: 29 AF XY: 0.0466 AC XY: 33758AN XY: 724716
GnomAD4 genome AF: 0.0376 AC: 5724AN: 152236Hom.: 154 Cov.: 32 AF XY: 0.0380 AC XY: 2826AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at