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GeneBe

rs963336

Variant summary

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

The ENST00000649832.1(null):n.510+4236A>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 0.546 in 152,012 control chromosomes in the GnomAD database, including 22,973 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 0.55 ( 22973 hom., cov: 31)

Consequence


ENST00000649832.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.370
Variant links:
Genes affected

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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 (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000649832.1 linkuse as main transcriptn.510+4236A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.546
AC:
82895
AN:
151892
Hom.:
22961
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.619
Gnomad AMI
AF:
0.515
Gnomad AMR
AF:
0.438
Gnomad ASJ
AF:
0.601
Gnomad EAS
AF:
0.497
Gnomad SAS
AF:
0.546
Gnomad FIN
AF:
0.532
Gnomad MID
AF:
0.528
Gnomad NFE
AF:
0.529
Gnomad OTH
AF:
0.534
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.546
AC:
82949
AN:
152012
Hom.:
22973
Cov.:
31
AF XY:
0.543
AC XY:
40376
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.619
Gnomad4 AMR
AF:
0.438
Gnomad4 ASJ
AF:
0.601
Gnomad4 EAS
AF:
0.496
Gnomad4 SAS
AF:
0.544
Gnomad4 FIN
AF:
0.532
Gnomad4 NFE
AF:
0.529
Gnomad4 OTH
AF:
0.536
Alfa
AF:
0.522
Hom.:
3568
Bravo
AF:
0.541
Asia WGS
AF:
0.576
AC:
2006
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
2.6
Dann
Benign
0.56

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: rs963336; hg19: chr10-12924440; API