rs2867161

Variant summary

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

The ENST00000446187.2(ENSG00000226829):​n.465+12435G>T 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 0.113 in 152,076 control chromosomes in the GnomAD database, including 1,005 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 0.11 ( 1005 hom., cov: 32)

Consequence


ENST00000446187.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.60
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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105375341XR_927643.4 linkuse as main transcriptn.508+12435G>T intron_variant, non_coding_transcript_variant
LOC105375341XR_927641.1 linkuse as main transcriptn.488-509G>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000446187.2 linkuse as main transcriptn.465+12435G>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.113
AC:
17097
AN:
151958
Hom.:
995
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.155
Gnomad AMI
AF:
0.209
Gnomad AMR
AF:
0.0775
Gnomad ASJ
AF:
0.0637
Gnomad EAS
AF:
0.0649
Gnomad SAS
AF:
0.145
Gnomad FIN
AF:
0.117
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.0966
Gnomad OTH
AF:
0.108
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.113
AC:
17144
AN:
152076
Hom.:
1005
Cov.:
32
AF XY:
0.114
AC XY:
8481
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.155
Gnomad4 AMR
AF:
0.0774
Gnomad4 ASJ
AF:
0.0637
Gnomad4 EAS
AF:
0.0649
Gnomad4 SAS
AF:
0.146
Gnomad4 FIN
AF:
0.117
Gnomad4 NFE
AF:
0.0966
Gnomad4 OTH
AF:
0.113
Alfa
AF:
0.0917
Hom.:
794
Bravo
AF:
0.110
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
-0.92
CADD
Benign
0.014
DANN
Benign
0.37

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: rs2867161; hg19: chr7-67637342; API