rs574281511
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_198525.3(KIF7):c.3192A>T(p.Thr1064=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000416 in 1,608,836 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T1064T) has been classified as Likely benign.
Frequency
Consequence
NM_198525.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF7 | NM_198525.3 | c.3192A>T | p.Thr1064= | synonymous_variant | 16/19 | ENST00000394412.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF7 | ENST00000394412.8 | c.3192A>T | p.Thr1064= | synonymous_variant | 16/19 | 5 | NM_198525.3 | P2 | |
TICRR | ENST00000561095.1 | c.*1080T>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 1 | ||||
KIF7 | ENST00000696512.1 | c.3315A>T | p.Thr1105= | synonymous_variant | 16/19 | A2 | |||
KIF7 | ENST00000677187.1 | n.866A>T | non_coding_transcript_exon_variant | 4/7 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000505 AC: 12AN: 237854Hom.: 0 AF XY: 0.0000544 AC XY: 7AN XY: 128580
GnomAD4 exome AF: 0.0000364 AC: 53AN: 1456482Hom.: 0 Cov.: 31 AF XY: 0.0000387 AC XY: 28AN XY: 723896
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74506
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Acrocallosal syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at