rs7578199
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005336.6(HDLBP):āc.1253A>Gā(p.Asn418Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 1,610,946 control chromosomes in the GnomAD database, including 40,645 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005336.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HDLBP | NM_005336.6 | c.1253A>G | p.Asn418Ser | missense_variant | 10/28 | ENST00000310931.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HDLBP | ENST00000310931.10 | c.1253A>G | p.Asn418Ser | missense_variant | 10/28 | 1 | NM_005336.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.209 AC: 31715AN: 152030Hom.: 3605 Cov.: 32
GnomAD3 exomes AF: 0.186 AC: 46672AN: 251434Hom.: 5386 AF XY: 0.186 AC XY: 25330AN XY: 135894
GnomAD4 exome AF: 0.215 AC: 314337AN: 1458798Hom.: 37040 Cov.: 31 AF XY: 0.213 AC XY: 154864AN XY: 725912
GnomAD4 genome AF: 0.208 AC: 31713AN: 152148Hom.: 3605 Cov.: 32 AF XY: 0.206 AC XY: 15317AN XY: 74364
ClinVar
Submissions by phenotype
HDLBP-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at