chr2-218281940-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_022152.6(TMBIM1):c.202G>A(p.Gly68Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00331 in 1,592,592 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_022152.6 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMBIM1 | NM_022152.6 | c.202G>A | p.Gly68Ser | missense_variant, splice_region_variant | 2/12 | ENST00000258412.8 | |
PNKD | NM_015488.5 | c.236+10391C>T | intron_variant | ENST00000273077.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMBIM1 | ENST00000258412.8 | c.202G>A | p.Gly68Ser | missense_variant, splice_region_variant | 2/12 | 1 | NM_022152.6 | P1 | |
PNKD | ENST00000273077.9 | c.236+10391C>T | intron_variant | 1 | NM_015488.5 |
Frequencies
GnomAD3 genomes AF: 0.00292 AC: 445AN: 152154Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00302 AC: 641AN: 211960Hom.: 2 AF XY: 0.00311 AC XY: 358AN XY: 114928
GnomAD4 exome AF: 0.00335 AC: 4822AN: 1440320Hom.: 19 Cov.: 31 AF XY: 0.00335 AC XY: 2390AN XY: 714414
GnomAD4 genome AF: 0.00292 AC: 444AN: 152272Hom.: 3 Cov.: 32 AF XY: 0.00271 AC XY: 202AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | PNKD: BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at