5-122020284-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152546.3(SRFBP1):c.549T>A(p.Asn183Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000548 in 1,459,684 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_152546.3 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 |
---|---|---|---|---|---|---|---|
SRFBP1 | NM_152546.3 | c.549T>A | p.Asn183Lys | missense_variant | 6/8 | ENST00000339397.5 | |
SRFBP1 | XM_017009111.3 | c.549T>A | p.Asn183Lys | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRFBP1 | ENST00000339397.5 | c.549T>A | p.Asn183Lys | missense_variant | 6/8 | 1 | NM_152546.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000811 AC: 2AN: 246642Hom.: 0 AF XY: 0.00000748 AC XY: 1AN XY: 133738
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1459684Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 6AN XY: 726070
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.549T>A (p.N183K) alteration is located in exon 6 (coding exon 6) of the SRFBP1 gene. This alteration results from a T to A substitution at nucleotide position 549, causing the asparagine (N) at amino acid position 183 to be replaced by a lysine (K). 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