rs10199680
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001378454.1(ALMS1):c.9782-9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00639 in 1,612,400 control chromosomes in the GnomAD database, including 556 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001378454.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0336 AC: 5110AN: 152034Hom.: 287 Cov.: 33
GnomAD3 exomes AF: 0.00869 AC: 2165AN: 249192Hom.: 126 AF XY: 0.00621 AC XY: 840AN XY: 135208
GnomAD4 exome AF: 0.00353 AC: 5152AN: 1460248Hom.: 264 Cov.: 31 AF XY: 0.00303 AC XY: 2201AN XY: 726562
GnomAD4 genome AF: 0.0338 AC: 5144AN: 152152Hom.: 292 Cov.: 33 AF XY: 0.0329 AC XY: 2447AN XY: 74382
ClinVar
Submissions by phenotype
not specified Benign:2
c.9779-9C>T in intron 11 of ALMS1: This variant is not expected to have clinical significance because a C>T change at this position does not diverge from the sp lice consensus sequence and is therefore unlikely to impact splicing. It has bee n identified in 12.00% (1176/9796) of African chromosomes by the Exome Aggregati on Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs10199680). -
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not provided Benign:2
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Alstrom syndrome Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at