chr12-53192471-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000889.3(ITGB7):c.2014C>T(p.His672Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0116 in 1,614,176 control chromosomes in the GnomAD database, including 124 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 (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_000889.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00870 AC: 1324AN: 152186Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00841 AC: 2110AN: 250872Hom.: 8 AF XY: 0.00883 AC XY: 1198AN XY: 135644
GnomAD4 exome AF: 0.0119 AC: 17341AN: 1461872Hom.: 119 Cov.: 31 AF XY: 0.0116 AC XY: 8452AN XY: 727240
GnomAD4 genome AF: 0.00871 AC: 1326AN: 152304Hom.: 5 Cov.: 32 AF XY: 0.00815 AC XY: 607AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 21, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at