rs7797223

Variant summary

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

The ENST00000439694.5(ENSG00000234352):​n.344-77265T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,158 control chromosomes in the GnomAD database, including 4,990 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 0.25 ( 4990 hom., cov: 33)

Consequence

ENSG00000234352
ENST00000439694.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0770
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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000234352ENST00000439694.5 linkn.344-77265T>A intron_variant Intron 3 of 3 1
ENSG00000234352ENST00000586239.5 linkn.274-77265T>A intron_variant Intron 2 of 4 5
ENSG00000234352ENST00000592183.5 linkn.475-77265T>A intron_variant Intron 3 of 3 4

Frequencies

GnomAD3 genomes
AF:
0.245
AC:
37313
AN:
152040
Hom.:
4984
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.320
Gnomad AMI
AF:
0.340
Gnomad AMR
AF:
0.194
Gnomad ASJ
AF:
0.211
Gnomad EAS
AF:
0.0121
Gnomad SAS
AF:
0.123
Gnomad FIN
AF:
0.190
Gnomad MID
AF:
0.212
Gnomad NFE
AF:
0.248
Gnomad OTH
AF:
0.229
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.245
AC:
37337
AN:
152158
Hom.:
4990
Cov.:
33
AF XY:
0.237
AC XY:
17647
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.320
Gnomad4 AMR
AF:
0.194
Gnomad4 ASJ
AF:
0.211
Gnomad4 EAS
AF:
0.0120
Gnomad4 SAS
AF:
0.123
Gnomad4 FIN
AF:
0.190
Gnomad4 NFE
AF:
0.248
Gnomad4 OTH
AF:
0.227
Alfa
AF:
0.250
Hom.:
617
Bravo
AF:
0.249
Asia WGS
AF:
0.0760
AC:
266
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
1.5
DANN
Benign
0.38

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: rs7797223; hg19: chr7-136547903; API