11-39887112-T-C

Variant summary

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

The XR_001748194.1(LOC105376637):​n.58+76049A>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 0.102 in 151,720 control chromosomes in the GnomAD database, including 999 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 0.10 ( 999 hom., cov: 31)

Consequence

LOC105376637
XR_001748194.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.462
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=-0.94).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105376637XR_001748194.1 linkuse as main transcriptn.58+76049A>G intron_variant, non_coding_transcript_variant
LOC105376637XR_001748195.2 linkuse as main transcriptn.58+76049A>G intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.102
AC:
15513
AN:
151614
Hom.:
996
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0456
Gnomad AMI
AF:
0.171
Gnomad AMR
AF:
0.100
Gnomad ASJ
AF:
0.178
Gnomad EAS
AF:
0.00154
Gnomad SAS
AF:
0.0549
Gnomad FIN
AF:
0.0828
Gnomad MID
AF:
0.196
Gnomad NFE
AF:
0.145
Gnomad OTH
AF:
0.141
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.102
AC:
15521
AN:
151720
Hom.:
999
Cov.:
31
AF XY:
0.0994
AC XY:
7373
AN XY:
74140
show subpopulations
Gnomad4 AFR
AF:
0.0455
Gnomad4 AMR
AF:
0.100
Gnomad4 ASJ
AF:
0.178
Gnomad4 EAS
AF:
0.00155
Gnomad4 SAS
AF:
0.0554
Gnomad4 FIN
AF:
0.0828
Gnomad4 NFE
AF:
0.145
Gnomad4 OTH
AF:
0.142
Alfa
AF:
0.139
Hom.:
1630
Bravo
AF:
0.103
Asia WGS
AF:
0.0480
AC:
168
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.26
DANN
Benign
0.74

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: rs11035577; hg19: chr11-39908662; API