7-93886846-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_006528.4(TFPI2):c.682C>T(p.Arg228Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000787 in 1,552,370 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_006528.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TFPI2 | NM_006528.4 | c.682C>T | p.Arg228Trp | missense_variant | 5/5 | ENST00000222543.11 | NP_006519.1 | |
TFPI2 | NM_001271003.2 | c.649C>T | p.Arg217Trp | missense_variant | 5/5 | NP_001257932.1 | ||
TFPI2 | NM_001271004.2 | c.*45C>T | 3_prime_UTR_variant | 5/5 | NP_001257933.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TFPI2 | ENST00000222543.11 | c.682C>T | p.Arg228Trp | missense_variant | 5/5 | 1 | NM_006528.4 | ENSP00000222543.5 | ||
TFPI2 | ENST00000650573.1 | c.700C>T | p.Arg234Trp | missense_variant | 5/5 | ENSP00000497131.1 | ||||
TFPI2 | ENST00000451238.1 | c.*45C>T | 3_prime_UTR_variant | 4/4 | 2 | ENSP00000416370.1 | ||||
GNGT1 | ENST00000455502.5 | c.-12+297G>A | intron_variant | 2 | ENSP00000395857.1 |
Frequencies
GnomAD3 genomes AF: 0.00425 AC: 646AN: 152022Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00109 AC: 211AN: 193072Hom.: 1 AF XY: 0.000825 AC XY: 88AN XY: 106642
GnomAD4 exome AF: 0.000410 AC: 574AN: 1400230Hom.: 2 Cov.: 30 AF XY: 0.000363 AC XY: 253AN XY: 696050
GnomAD4 genome AF: 0.00425 AC: 647AN: 152140Hom.: 5 Cov.: 32 AF XY: 0.00429 AC XY: 319AN XY: 74382
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 16, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at