chr9-109216946-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019114.5(EPB41L4B):c.1609A>G(p.Asn537Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,614,156 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019114.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPB41L4B | NM_019114.5 | c.1609A>G | p.Asn537Asp | missense_variant | 16/26 | ENST00000374566.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPB41L4B | ENST00000374566.8 | c.1609A>G | p.Asn537Asp | missense_variant | 16/26 | 1 | NM_019114.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000236 AC: 36AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000255 AC: 63AN: 247052Hom.: 1 AF XY: 0.000268 AC XY: 36AN XY: 134240
GnomAD4 exome AF: 0.0000937 AC: 137AN: 1461814Hom.: 1 Cov.: 32 AF XY: 0.000105 AC XY: 76AN XY: 727206
GnomAD4 genome ? AF: 0.000236 AC: 36AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74500
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2023 | The c.1609A>G (p.N537D) alteration is located in exon 16 (coding exon 16) of the EPB41L4B gene. This alteration results from a A to G substitution at nucleotide position 1609, causing the asparagine (N) at amino acid position 537 to be replaced by an aspartic acid (D). 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