chr2-186640975-T-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_002210.5(ITGAV):c.956+8T>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00153 in 1,565,206 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_002210.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGAV | NM_002210.5 | c.956+8T>A | splice_region_variant, intron_variant | ENST00000261023.8 | |||
ITGAV | NM_001144999.3 | c.818+8T>A | splice_region_variant, intron_variant | ||||
ITGAV | NM_001145000.3 | c.848+8T>A | splice_region_variant, intron_variant | ||||
ITGAV | XM_047444225.1 | c.113+8T>A | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGAV | ENST00000261023.8 | c.956+8T>A | splice_region_variant, intron_variant | 1 | NM_002210.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00831 AC: 1259AN: 151434Hom.: 20 Cov.: 32
GnomAD3 exomes AF: 0.00234 AC: 449AN: 192274Hom.: 4 AF XY: 0.00174 AC XY: 180AN XY: 103592
GnomAD4 exome AF: 0.000808 AC: 1142AN: 1413660Hom.: 12 Cov.: 27 AF XY: 0.000705 AC XY: 495AN XY: 701754
GnomAD4 genome AF: 0.00829 AC: 1256AN: 151546Hom.: 20 Cov.: 32 AF XY: 0.00793 AC XY: 587AN XY: 74040
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 01, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at