chr7-91538287-A-G

Variant summary

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

The ENST00000456952.1(ENSG00000235450):​n.112+18450T>C 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 0.17 in 152,196 control chromosomes in the GnomAD database, including 2,494 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 0.17 ( 2494 hom., cov: 32)

Consequence


ENST00000456952.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.730
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=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000456952.1 linkuse as main transcriptn.112+18450T>C intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.170
AC:
25812
AN:
152078
Hom.:
2490
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0983
Gnomad AMI
AF:
0.132
Gnomad AMR
AF:
0.162
Gnomad ASJ
AF:
0.276
Gnomad EAS
AF:
0.0635
Gnomad SAS
AF:
0.167
Gnomad FIN
AF:
0.192
Gnomad MID
AF:
0.266
Gnomad NFE
AF:
0.214
Gnomad OTH
AF:
0.188
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.170
AC:
25818
AN:
152196
Hom.:
2494
Cov.:
32
AF XY:
0.168
AC XY:
12467
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.0983
Gnomad4 AMR
AF:
0.162
Gnomad4 ASJ
AF:
0.276
Gnomad4 EAS
AF:
0.0634
Gnomad4 SAS
AF:
0.168
Gnomad4 FIN
AF:
0.192
Gnomad4 NFE
AF:
0.214
Gnomad4 OTH
AF:
0.185
Alfa
AF:
0.211
Hom.:
4187
Bravo
AF:
0.166
Asia WGS
AF:
0.0980
AC:
341
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.41
DANN
Benign
0.45

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: rs17691129; hg19: chr7-91167602; API