chr3-186619924-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001622.4(AHSG):āc.743T>Cā(p.Met248Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 1,611,398 control chromosomes in the GnomAD database, including 358,503 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_001622.4 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 |
---|---|---|---|---|---|---|---|
AHSG | NM_001622.4 | c.743T>C | p.Met248Thr | missense_variant | 6/7 | ENST00000411641.7 | |
AHSG | NM_001354571.2 | c.746T>C | p.Met249Thr | missense_variant | 6/7 | ||
AHSG | NM_001354572.2 | c.740T>C | p.Met247Thr | missense_variant | 6/7 | ||
AHSG | NM_001354573.2 | c.676-662T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AHSG | ENST00000411641.7 | c.743T>C | p.Met248Thr | missense_variant | 6/7 | 1 | NM_001622.4 | P3 | |
HRG-AS1 | ENST00000630178.2 | n.239-39958A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.684 AC: 103930AN: 151990Hom.: 35853 Cov.: 31
GnomAD3 exomes AF: 0.676 AC: 168819AN: 249888Hom.: 57878 AF XY: 0.685 AC XY: 92597AN XY: 135138
GnomAD4 exome AF: 0.663 AC: 966968AN: 1459290Hom.: 322627 Cov.: 38 AF XY: 0.668 AC XY: 484685AN XY: 726042
GnomAD4 genome AF: 0.684 AC: 104002AN: 152108Hom.: 35876 Cov.: 31 AF XY: 0.684 AC XY: 50859AN XY: 74372
ClinVar
Submissions by phenotype
Alopecia-intellectual disability syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
RECLASSIFIED - ALPHA-2-HS-GLYCOPROTEIN POLYMORPHISM Benign:1
Benign, no assertion criteria provided | literature only | OMIM | Jun 01, 2005 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at