rs10776775

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_125965.1(AP4B1-AS1):​n.415-4008G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,054 control chromosomes in the GnomAD database, including 9,533 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.32 ( 9533 hom., cov: 33)

Consequence

AP4B1-AS1
NR_125965.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.116
Variant links:
Genes affected
AP4B1-AS1 (HGNC:44114): (AP4B1 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AP4B1-AS1NR_125965.1 linkuse as main transcriptn.415-4008G>A intron_variant, non_coding_transcript_variant
AP4B1-AS1NR_037864.1 linkuse as main transcriptn.247-4008G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AP4B1-AS1ENST00000419536.1 linkuse as main transcriptn.247-4008G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.322
AC:
48934
AN:
151936
Hom.:
9540
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.129
Gnomad AMI
AF:
0.338
Gnomad AMR
AF:
0.461
Gnomad ASJ
AF:
0.277
Gnomad EAS
AF:
0.778
Gnomad SAS
AF:
0.269
Gnomad FIN
AF:
0.442
Gnomad MID
AF:
0.307
Gnomad NFE
AF:
0.360
Gnomad OTH
AF:
0.342
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.322
AC:
48938
AN:
152054
Hom.:
9533
Cov.:
33
AF XY:
0.330
AC XY:
24503
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.129
Gnomad4 AMR
AF:
0.461
Gnomad4 ASJ
AF:
0.277
Gnomad4 EAS
AF:
0.777
Gnomad4 SAS
AF:
0.269
Gnomad4 FIN
AF:
0.442
Gnomad4 NFE
AF:
0.360
Gnomad4 OTH
AF:
0.344
Alfa
AF:
0.353
Hom.:
11088
Bravo
AF:
0.324
Asia WGS
AF:
0.489
AC:
1700
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.35
DANN
Benign
0.57

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: rs10776775; hg19: chr1-114436482; API