rs7913069

Variant summary

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

The ENST00000698306.1(ENSG00000289745):​n.223+5122G>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 0.0693 in 152,116 control chromosomes in the GnomAD database, including 640 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 0.069 ( 640 hom., cov: 32)

Consequence


ENST00000698306.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.137
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 (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC102724351XR_007062282.1 linkuse as main transcriptn.1431+3818G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000698306.1 linkuse as main transcriptn.223+5122G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0691
AC:
10506
AN:
151998
Hom.:
637
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.148
Gnomad AMI
AF:
0.0297
Gnomad AMR
AF:
0.0959
Gnomad ASJ
AF:
0.0161
Gnomad EAS
AF:
0.0820
Gnomad SAS
AF:
0.0705
Gnomad FIN
AF:
0.0694
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.0172
Gnomad OTH
AF:
0.0675
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0693
AC:
10539
AN:
152116
Hom.:
640
Cov.:
32
AF XY:
0.0718
AC XY:
5341
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.149
Gnomad4 AMR
AF:
0.0963
Gnomad4 ASJ
AF:
0.0161
Gnomad4 EAS
AF:
0.0827
Gnomad4 SAS
AF:
0.0704
Gnomad4 FIN
AF:
0.0694
Gnomad4 NFE
AF:
0.0172
Gnomad4 OTH
AF:
0.0663
Alfa
AF:
0.0273
Hom.:
198
Bravo
AF:
0.0753
Asia WGS
AF:
0.0970
AC:
338
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
2.9
DANN
Benign
0.62

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: rs7913069; hg19: chr10-105714399; API