chr19-55762006-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001145014.2(RFPL4A):c.206C>T(p.Ala69Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000273 in 146,446 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145014.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000273 AC: 40AN: 146336Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000212 AC: 32AN: 150640Hom.: 0 AF XY: 0.000225 AC XY: 18AN XY: 79946
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000195 AC: 266AN: 1363472Hom.: 0 Cov.: 34 AF XY: 0.000201 AC XY: 135AN XY: 672694
GnomAD4 genome AF: 0.000273 AC: 40AN: 146446Hom.: 0 Cov.: 30 AF XY: 0.000294 AC XY: 21AN XY: 71516
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.206C>T (p.A69V) alteration is located in exon 2 (coding exon 1) of the RFPL4A gene. This alteration results from a C to T substitution at nucleotide position 206, causing the alanine (A) at amino acid position 69 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at