6-166329529-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_145169.3(SFT2D1):c.211G>A(p.Gly71Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000343 in 1,456,418 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. G71D) has been classified as Uncertain significance.
Frequency
Consequence
NM_145169.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFT2D1 | NM_145169.3 | c.211G>A | p.Gly71Ser | missense_variant | 3/8 | ENST00000361731.4 | |
SFT2D1 | NR_130112.2 | n.298G>A | non_coding_transcript_exon_variant | 4/9 | |||
SFT2D1 | NR_130113.2 | n.298G>A | non_coding_transcript_exon_variant | 4/7 | |||
SFT2D1 | NR_130114.2 | n.289G>A | non_coding_transcript_exon_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFT2D1 | ENST00000361731.4 | c.211G>A | p.Gly71Ser | missense_variant | 3/8 | 1 | NM_145169.3 | P1 | |
SFT2D1 | ENST00000487841.5 | n.300G>A | non_coding_transcript_exon_variant | 4/8 | 1 | ||||
SFT2D1 | ENST00000478705.5 | n.329G>A | non_coding_transcript_exon_variant | 4/9 | 2 | ||||
SFT2D1 | ENST00000488773.1 | n.171G>A | non_coding_transcript_exon_variant | 3/6 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1456418Hom.: 0 Cov.: 30 AF XY: 0.00000276 AC XY: 2AN XY: 724480
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2022 | The c.211G>A (p.G71S) alteration is located in exon 3 (coding exon 3) of the SFT2D1 gene. This alteration results from a G to A substitution at nucleotide position 211, causing the glycine (G) at amino acid position 71 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