rs2228220
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002114.4(HIVEP1):āc.3221A>Gā(p.Asn1074Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 1,613,994 control chromosomes in the GnomAD database, including 9,228 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_002114.4 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 |
---|---|---|---|---|---|---|---|
HIVEP1 | NM_002114.4 | c.3221A>G | p.Asn1074Ser | missense_variant | 4/9 | ENST00000379388.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIVEP1 | ENST00000379388.7 | c.3221A>G | p.Asn1074Ser | missense_variant | 4/9 | 1 | NM_002114.4 | P2 | |
HIVEP1 | ENST00000541134.5 | c.3221A>G | p.Asn1074Ser | missense_variant | 4/9 | 5 | A2 | ||
HIVEP1 | ENST00000627968.2 | c.-3083A>G | 5_prime_UTR_variant | 4/8 | 5 | ||||
HIVEP1 | ENST00000442081.6 | c.166+3082A>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.115 AC: 17415AN: 152090Hom.: 1133 Cov.: 32
GnomAD3 exomes AF: 0.106 AC: 26502AN: 249158Hom.: 1623 AF XY: 0.110 AC XY: 14890AN XY: 135194
GnomAD4 exome AF: 0.100 AC: 146625AN: 1461786Hom.: 8088 Cov.: 39 AF XY: 0.103 AC XY: 74817AN XY: 727184
GnomAD4 genome ? AF: 0.115 AC: 17452AN: 152208Hom.: 1140 Cov.: 32 AF XY: 0.113 AC XY: 8437AN XY: 74436
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at