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chr15-89908403-AGTAGCGCTCCTGGGGCCAGGCAGACAGAGAGTGAGGGGGCGGCTTCATCCCACAACACACACACTCTGGGCTCCGGCTGCAGCCCCGCCAACCTCACATCTACCCTAGAAGCCCACCTCAGCTCCAAAAGATGTTCAAGCTAGGCAGATGCTCCCTCTGCCCCCAAATACTTATGCATTCATGGGTTCACAAGAGCACCTGCCGCATATAATGAGCCCTGCTAGAAGTTCCTAACAGGGCAAGCCCAGGGCTTCCACACAGCCAAAGACAAAAAGTATATATAGAAAACCATAACTTGGGCTGGGCACAGTGGCTCACGTCTGTAATCCCAGCACTTTGGGAGGCAGTGGCGAGTGGATCACGAGGTCAGGAGTTCGAGACCAGCCTGGCCAGCATGGTGAAACCCTGTCTCCATCAAAAATATAAAAAATTAGCCAGGTGTGGTGGCATGTGCCTGTAATCCCAGCTATTCAGGAGGCTAAGGCAGGAGAATCGCTTGAGCCCAGGAGGCGGAGGTTGCTGTAAGCCGAGATCCTGCCACTGTACTCCAGCCGGGGAGACAGAATGAGACTTCATCTCAAAAAACAAAAACAAAACAAAACAAAACCATAACCCAAGCCCGAGGACCGCAAATACCATGAAGCAGGAATGGGCGCTGCCAAGGTGCAATGGAAAGGGCACTGAAAAGGAGCCCTGGGTGAGGGCAGCCACTCTGCCCCTTCCAACAGCCTGGGACAAACCACTCAGTTTCCCCATCACATGGGGATAACGTGATGTCTGTGTTTAAGAATATTATGAGGGTTCAATGAGATAACAGAGGGGCAAGCACAGTGCCAAGCGTGAACTGTGCTATAAGTGCTGTTTGCCAGTTGTTCAAGGCAGGTGGGTGAAATGCTCCCAGGGCCTGAAGAATAGGAGGCCACATCCTGGTGGAATCAAGAAAGATGAAGTCTTGGAGGGTAGGGAGGTCTG-A

Position:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_182616.4(ARPIN):​c.169-963_177del variant causes a splice acceptor, coding sequence, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

ARPIN
NM_182616.4 splice_acceptor, coding_sequence, intron

Scores

Not classified

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 7.27
Variant links:
Genes affected
ARPIN (HGNC:28782): (actin related protein 2/3 complex inhibitor) Involved in directional locomotion; negative regulation of cell migration; and negative regulation of cellular component organization. Predicted to be located in lamellipodium. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ARPINNM_182616.4 linkuse as main transcriptc.169-963_177del splice_acceptor_variant, coding_sequence_variant, intron_variant 3/6 ENST00000357484.10
ARPIN-AP3S2NM_001199058.2 linkuse as main transcriptc.169-963_177del splice_acceptor_variant, coding_sequence_variant, intron_variant 3/10
ARPINNM_001282380.2 linkuse as main transcriptc.-120-963_-112del splice_acceptor_variant, 5_prime_UTR_variant, intron_variant 3/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ARPINENST00000357484.10 linkuse as main transcriptc.169-963_177del splice_acceptor_variant, coding_sequence_variant, intron_variant 3/61 NM_182616.4 P1Q7Z6K5-1
ARPINENST00000460685.1 linkuse as main transcriptc.-120-963_-112del splice_acceptor_variant, 5_prime_UTR_variant, intron_variant 3/62

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Seizure Uncertain:1
Uncertain significance, no assertion criteria providedclinical testingNew York Genome CenterDec 24, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1897164637; hg19: chr15-90451635; API