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GeneBe

rs11763963

Variant summary

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

The ENST00000661238.1(ENSG00000286507):n.49-2297A>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 0.0575 in 152,172 control chromosomes in the GnomAD database, including 406 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 0.058 ( 406 hom., cov: 32)

Consequence


ENST00000661238.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.39
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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC101928077XR_007060264.1 linkuse as main transcriptn.1167-6444A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000661238.1 linkuse as main transcriptn.49-2297A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0576
AC:
8756
AN:
152054
Hom.:
407
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0168
Gnomad AMI
AF:
0.116
Gnomad AMR
AF:
0.0486
Gnomad ASJ
AF:
0.0825
Gnomad EAS
AF:
0.245
Gnomad SAS
AF:
0.0854
Gnomad FIN
AF:
0.0839
Gnomad MID
AF:
0.0955
Gnomad NFE
AF:
0.0617
Gnomad OTH
AF:
0.0609
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0575
AC:
8751
AN:
152172
Hom.:
406
Cov.:
32
AF XY:
0.0589
AC XY:
4381
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.0168
Gnomad4 AMR
AF:
0.0485
Gnomad4 ASJ
AF:
0.0825
Gnomad4 EAS
AF:
0.245
Gnomad4 SAS
AF:
0.0861
Gnomad4 FIN
AF:
0.0839
Gnomad4 NFE
AF:
0.0617
Gnomad4 OTH
AF:
0.0593
Alfa
AF:
0.0558
Hom.:
33
Bravo
AF:
0.0536
Asia WGS
AF:
0.139
AC:
483
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
Cadd
Benign
0.93
Dann
Benign
0.57

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: rs11763963; hg19: chr7-26645433; API