chr6-40392461-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_020737.3(LRFN2):c.1852G>T(p.Ala618Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000392 in 1,567,400 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A618T) has been classified as Uncertain significance.
Frequency
Consequence
NM_020737.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRFN2 | NM_020737.3 | c.1852G>T | p.Ala618Ser | missense_variant | 3/3 | ENST00000338305.7 | |
LRFN2 | XM_011514762.3 | c.1852G>T | p.Ala618Ser | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRFN2 | ENST00000338305.7 | c.1852G>T | p.Ala618Ser | missense_variant | 3/3 | 1 | NM_020737.3 | P1 | |
LRFN2 | ENST00000700335.1 | c.1852G>T | p.Ala618Ser | missense_variant | 4/4 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000165 AC: 27AN: 163930Hom.: 1 AF XY: 0.000123 AC XY: 11AN XY: 89664
GnomAD4 exome AF: 0.000412 AC: 583AN: 1415152Hom.: 1 Cov.: 34 AF XY: 0.000371 AC XY: 260AN XY: 700296
GnomAD4 genome AF: 0.000204 AC: 31AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.1852G>T (p.A618S) alteration is located in exon 3 (coding exon 2) of the LRFN2 gene. This alteration results from a G to T substitution at nucleotide position 1852, causing the alanine (A) at amino acid position 618 to be replaced by a serine (S). 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