rs921348

Variant summary

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

The NR_038943.1(ADD3-AS1):​n.463-464T>C 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 0.224 in 152,072 control chromosomes in the GnomAD database, including 4,605 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 0.22 ( 4605 hom., cov: 32)

Consequence

ADD3-AS1
NR_038943.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.92
Variant links:
Genes affected
ADD3-AS1 (HGNC:48682): (ADD3 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=-0.64).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ADD3-AS1NR_038943.1 linkuse as main transcriptn.463-464T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADD3-AS1ENST00000627565.2 linkuse as main transcriptn.590-464T>C intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.224
AC:
34046
AN:
151954
Hom.:
4597
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.334
Gnomad AMI
AF:
0.0967
Gnomad AMR
AF:
0.148
Gnomad ASJ
AF:
0.212
Gnomad EAS
AF:
0.403
Gnomad SAS
AF:
0.491
Gnomad FIN
AF:
0.146
Gnomad MID
AF:
0.237
Gnomad NFE
AF:
0.157
Gnomad OTH
AF:
0.217
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.224
AC:
34084
AN:
152072
Hom.:
4605
Cov.:
32
AF XY:
0.229
AC XY:
17059
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.333
Gnomad4 AMR
AF:
0.148
Gnomad4 ASJ
AF:
0.212
Gnomad4 EAS
AF:
0.403
Gnomad4 SAS
AF:
0.493
Gnomad4 FIN
AF:
0.146
Gnomad4 NFE
AF:
0.157
Gnomad4 OTH
AF:
0.219
Alfa
AF:
0.187
Hom.:
1960
Bravo
AF:
0.221
Asia WGS
AF:
0.441
AC:
1533
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.64
CADD
Benign
15
DANN
Benign
0.65

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: rs921348; hg19: chr10-111707498; API