rs17079195

Variant summary

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

The ENST00000661028.1(ENSG00000287907):​n.255+24222T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,180 control chromosomes in the GnomAD database, including 2,361 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 0.16 ( 2361 hom., cov: 32)

Consequence

ENSG00000287907
ENST00000661028.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.412
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=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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
ENSG00000287907ENST00000661028.1 linkn.255+24222T>G intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.164
AC:
24915
AN:
152062
Hom.:
2354
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.210
Gnomad AMI
AF:
0.0910
Gnomad AMR
AF:
0.137
Gnomad ASJ
AF:
0.301
Gnomad EAS
AF:
0.408
Gnomad SAS
AF:
0.173
Gnomad FIN
AF:
0.142
Gnomad MID
AF:
0.250
Gnomad NFE
AF:
0.120
Gnomad OTH
AF:
0.169
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.164
AC:
24939
AN:
152180
Hom.:
2361
Cov.:
32
AF XY:
0.168
AC XY:
12505
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.210
Gnomad4 AMR
AF:
0.137
Gnomad4 ASJ
AF:
0.301
Gnomad4 EAS
AF:
0.407
Gnomad4 SAS
AF:
0.174
Gnomad4 FIN
AF:
0.142
Gnomad4 NFE
AF:
0.120
Gnomad4 OTH
AF:
0.169
Alfa
AF:
0.139
Hom.:
3508
Bravo
AF:
0.167
Asia WGS
AF:
0.258
AC:
895
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.43
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: rs17079195; hg19: chr18-66137894; API