rs491996

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.188+73133T>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 0.128 in 152,088 control chromosomes in the GnomAD database, including 1,761 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 0.13 ( 1761 hom., cov: 32)

Consequence


ENST00000662551.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.532
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=-0.81).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124900354XR_001751516.3 linkuse as main transcriptn.142+1545T>A intron_variant, non_coding_transcript_variant
LOC124900354XR_001751517.2 linkuse as main transcriptn.142+1545T>A intron_variant, non_coding_transcript_variant
LOC124900354XR_007064618.1 linkuse as main transcriptn.142+1545T>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000662551.1 linkuse as main transcriptn.188+73133T>A intron_variant, non_coding_transcript_variant
ENST00000560900.1 linkuse as main transcriptn.195+1545T>A intron_variant, non_coding_transcript_variant 4
ENST00000664705.1 linkuse as main transcriptn.188+73133T>A intron_variant, non_coding_transcript_variant
ENST00000665188.1 linkuse as main transcriptn.68+73133T>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.127
AC:
19363
AN:
151970
Hom.:
1750
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.192
Gnomad AMI
AF:
0.182
Gnomad AMR
AF:
0.160
Gnomad ASJ
AF:
0.0360
Gnomad EAS
AF:
0.346
Gnomad SAS
AF:
0.276
Gnomad FIN
AF:
0.0709
Gnomad MID
AF:
0.0573
Gnomad NFE
AF:
0.0674
Gnomad OTH
AF:
0.104
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.128
AC:
19415
AN:
152088
Hom.:
1761
Cov.:
32
AF XY:
0.131
AC XY:
9740
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.193
Gnomad4 AMR
AF:
0.161
Gnomad4 ASJ
AF:
0.0360
Gnomad4 EAS
AF:
0.346
Gnomad4 SAS
AF:
0.275
Gnomad4 FIN
AF:
0.0709
Gnomad4 NFE
AF:
0.0674
Gnomad4 OTH
AF:
0.110
Alfa
AF:
0.0394
Hom.:
39
Bravo
AF:
0.134

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
0.23
DANN
Benign
0.60

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: rs491996; hg19: chr15-48178246; API