chr19-6713251-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000064.4(C3):c.941C>T(p.Pro314Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 1,613,434 control chromosomes in the GnomAD database, including 29,494 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000064.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.134 AC: 20348AN: 151964Hom.: 1874 Cov.: 31
GnomAD3 exomes AF: 0.141 AC: 35480AN: 250810Hom.: 3166 AF XY: 0.145 AC XY: 19674AN XY: 135634
GnomAD4 exome AF: 0.185 AC: 270924AN: 1461352Hom.: 27620 Cov.: 35 AF XY: 0.183 AC XY: 133204AN XY: 726968
GnomAD4 genome AF: 0.134 AC: 20349AN: 152082Hom.: 1874 Cov.: 31 AF XY: 0.131 AC XY: 9733AN XY: 74336
ClinVar
Submissions by phenotype
not provided Benign:3
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This variant is associated with the following publications: (PMID: 30131807, 19168221, 24736606, 24036950, 21784901, 25688879) -
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C3 POLYMORPHISM, HAV 4-1 PLUS/MINUS TYPE Benign:1
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Inborn genetic diseases 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. -
Age related macular degeneration 9 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -
Atypical hemolytic-uremic syndrome with C3 anomaly Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Focal segmental glomerulosclerosis Benign:1
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Complement component 3 deficiency Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at