rs6901992
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001198934.2(ABCC10):c.3713C>T(p.Thr1238Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00265 in 1,614,036 control chromosomes in the GnomAD database, including 78 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 (★).
Frequency
Consequence
NM_001198934.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC10 | NM_001198934.2 | c.3713C>T | p.Thr1238Ile | missense_variant | 18/22 | ENST00000372530.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC10 | ENST00000372530.9 | c.3713C>T | p.Thr1238Ile | missense_variant | 18/22 | 2 | NM_001198934.2 | P2 | |
ABCC10 | ENST00000244533.7 | c.3629C>T | p.Thr1210Ile | missense_variant | 16/20 | 1 | A2 | ||
ABCC10 | ENST00000437104.3 | n.562C>T | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
ABCC10 | ENST00000463024.1 | n.3441C>T | non_coding_transcript_exon_variant | 12/16 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0139 AC: 2115AN: 152206Hom.: 37 Cov.: 32
GnomAD3 exomes AF: 0.00367 AC: 912AN: 248822Hom.: 18 AF XY: 0.00277 AC XY: 374AN XY: 134876
GnomAD4 exome AF: 0.00147 AC: 2151AN: 1461712Hom.: 39 Cov.: 31 AF XY: 0.00135 AC XY: 985AN XY: 727160
GnomAD4 genome ? AF: 0.0139 AC: 2123AN: 152324Hom.: 39 Cov.: 32 AF XY: 0.0142 AC XY: 1055AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 30, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at