2-46956927-G-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001288955.2(TTC7A):c.-468G>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.00636 in 1,614,206 control chromosomes in the GnomAD database, including 58 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001288955.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00465 AC: 707AN: 152198Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00484 AC: 1217AN: 251492Hom.: 6 AF XY: 0.00504 AC XY: 685AN XY: 135920
GnomAD4 exome AF: 0.00654 AC: 9555AN: 1461890Hom.: 53 Cov.: 31 AF XY: 0.00643 AC XY: 4676AN XY: 727248
GnomAD4 genome AF: 0.00465 AC: 708AN: 152316Hom.: 5 Cov.: 33 AF XY: 0.00479 AC XY: 357AN XY: 74468
ClinVar
Submissions by phenotype
Multiple gastrointestinal atresias Uncertain:1Benign:1
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Gastrointestinal defects and immunodeficiency syndrome 1 Uncertain:1
TTC7A NM_020458.2 exon 3 p.Arg146Leu (c.437G>T): This variant has not been reported in the literature but is present in 0.6% (476/68038) of European alleles including 4 homozygotes in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/2-46956927-G-T?dataset=gnomad_r3). This variant is present in ClinVar (Variation ID:458800). Evolutionary conservation and computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. -
Inborn genetic diseases Uncertain:1
The c.437G>T (p.R146L) alteration is located in exon 3 (coding exon 3) of the TTC7A gene. This alteration results from a G to T substitution at nucleotide position 437, causing the arginine (R) at amino acid position 146 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Benign:1
TTC7A: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at