8-88361098-T-G

Variant summary

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

The ENST00000665922.1(ENSG00000253553):​n.193+32046T>G 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 0.203 in 151,706 control chromosomes in the GnomAD database, including 3,259 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 0.20 ( 3259 hom., cov: 31)

Consequence


ENST00000665922.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00
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=-1.0).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC105375630XR_001745653.3 linkuse as main transcriptn.224+32001T>G intron_variant, non_coding_transcript_variant
LOC105375630XR_007060996.1 linkuse as main transcriptn.179+32046T>G intron_variant, non_coding_transcript_variant
LOC105375630XR_007060997.1 linkuse as main transcriptn.123+32102T>G intron_variant, non_coding_transcript_variant
LOC105375630XR_007060998.1 linkuse as main transcriptn.179+32046T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000665922.1 linkuse as main transcriptn.193+32046T>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.203
AC:
30824
AN:
151590
Hom.:
3245
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.210
Gnomad AMI
AF:
0.357
Gnomad AMR
AF:
0.219
Gnomad ASJ
AF:
0.161
Gnomad EAS
AF:
0.0507
Gnomad SAS
AF:
0.230
Gnomad FIN
AF:
0.195
Gnomad MID
AF:
0.163
Gnomad NFE
AF:
0.206
Gnomad OTH
AF:
0.219
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.203
AC:
30871
AN:
151706
Hom.:
3259
Cov.:
31
AF XY:
0.202
AC XY:
14967
AN XY:
74182
show subpopulations
Gnomad4 AFR
AF:
0.211
Gnomad4 AMR
AF:
0.219
Gnomad4 ASJ
AF:
0.161
Gnomad4 EAS
AF:
0.0506
Gnomad4 SAS
AF:
0.229
Gnomad4 FIN
AF:
0.195
Gnomad4 NFE
AF:
0.206
Gnomad4 OTH
AF:
0.225
Alfa
AF:
0.170
Hom.:
754
Bravo
AF:
0.204
Asia WGS
AF:
0.195
AC:
675
AN:
3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.61
DANN
Benign
0.33

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: rs36116061; hg19: chr8-89373327; API