rs1431005

Variant summary

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

The NR_038931.1(LOC339975):​n.322+81078C>T 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 0.389 in 151,866 control chromosomes in the GnomAD database, including 11,671 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 0.39 ( 11671 hom., cov: 32)

Consequence

LOC339975
NR_038931.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.431
Variant links:
Genes affected

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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC339975NR_038931.1 linkuse as main transcriptn.322+81078C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.389
AC:
59097
AN:
151748
Hom.:
11662
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.365
Gnomad AMI
AF:
0.305
Gnomad AMR
AF:
0.337
Gnomad ASJ
AF:
0.383
Gnomad EAS
AF:
0.377
Gnomad SAS
AF:
0.383
Gnomad FIN
AF:
0.474
Gnomad MID
AF:
0.418
Gnomad NFE
AF:
0.405
Gnomad OTH
AF:
0.396
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.389
AC:
59125
AN:
151866
Hom.:
11671
Cov.:
32
AF XY:
0.390
AC XY:
28921
AN XY:
74208
show subpopulations
Gnomad4 AFR
AF:
0.365
Gnomad4 AMR
AF:
0.337
Gnomad4 ASJ
AF:
0.383
Gnomad4 EAS
AF:
0.378
Gnomad4 SAS
AF:
0.383
Gnomad4 FIN
AF:
0.474
Gnomad4 NFE
AF:
0.405
Gnomad4 OTH
AF:
0.392
Alfa
AF:
0.395
Hom.:
22777
Bravo
AF:
0.377
Asia WGS
AF:
0.370
AC:
1286
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.48
DANN
Benign
0.62

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: rs1431005; hg19: chr4-188345368; API