NM_000092.5:c.3963T>C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000092.5(COL4A4):āc.3963T>Cā(p.Asp1321Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00113 in 1,614,216 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_000092.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00590 AC: 898AN: 152216Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00157 AC: 392AN: 249190Hom.: 5 AF XY: 0.00118 AC XY: 159AN XY: 135240
GnomAD4 exome AF: 0.000632 AC: 924AN: 1461882Hom.: 11 Cov.: 32 AF XY: 0.000578 AC XY: 420AN XY: 727244
GnomAD4 genome AF: 0.00595 AC: 907AN: 152334Hom.: 11 Cov.: 32 AF XY: 0.00588 AC XY: 438AN XY: 74482
ClinVar
Submissions by phenotype
not specified Benign:4
p.Asp1321Asp in exon 41 of COL4A4: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wi thin the splice consensus sequence, and has been identified in 3.63% (48/1322) o f African chromosomes by the 1000 Genomes Project (Phase 3; dbSNP rs116124529). -
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not provided Benign:4
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Kidney disorder Benign:1
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Alport syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at