NM_031475.3:c.2061+7G>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_031475.3(ESPN):c.2061+7G>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 0.000686 in 1,611,518 control chromosomes in the GnomAD database, including 6 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 Likely benign (★★).
Frequency
Consequence
NM_031475.3 splice_region, 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: 0.000394 AC: 60AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00128 AC: 309AN: 241866Hom.: 1 AF XY: 0.00155 AC XY: 205AN XY: 132230
GnomAD4 exome AF: 0.000716 AC: 1045AN: 1459168Hom.: 6 Cov.: 32 AF XY: 0.000876 AC XY: 636AN XY: 725810
GnomAD4 genome AF: 0.000394 AC: 60AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.000550 AC XY: 41AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:4
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ESPN: BP4, BS2 -
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not specified Benign:1
c.2061+7G>A in intron 9 of ESPN: This variant is not expected to have clinical s ignificance because it has been identified in 0.9% (135/15134) of South Asian ch romosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute. org; rs369405672). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at