rs206626

Variant summary

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

The ENST00000669383.1(ENSG00000287065):​n.401-1673A>G 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 0.439 in 152,028 control chromosomes in the GnomAD database, including 17,016 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 0.44 ( 17016 hom., cov: 32)

Consequence


ENST00000669383.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.306
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 (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105371985XR_001753346.2 linkuse as main transcriptn.463+798T>C intron_variant, non_coding_transcript_variant
LOC105371985XR_001753345.2 linkuse as main transcriptn.653T>C non_coding_transcript_exon_variant 4/4
LOC105371985XR_007066287.1 linkuse as main transcriptn.552T>C non_coding_transcript_exon_variant 3/3
LOC105371985XR_001753344.2 linkuse as main transcriptn.532+798T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000669383.1 linkuse as main transcriptn.401-1673A>G intron_variant, non_coding_transcript_variant
ENST00000666410.1 linkuse as main transcript downstream_gene_variant

Frequencies

GnomAD3 genomes
AF:
0.440
AC:
66785
AN:
151910
Hom.:
17017
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.163
Gnomad AMI
AF:
0.476
Gnomad AMR
AF:
0.550
Gnomad ASJ
AF:
0.583
Gnomad EAS
AF:
0.684
Gnomad SAS
AF:
0.432
Gnomad FIN
AF:
0.540
Gnomad MID
AF:
0.561
Gnomad NFE
AF:
0.541
Gnomad OTH
AF:
0.473
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.439
AC:
66792
AN:
152028
Hom.:
17016
Cov.:
32
AF XY:
0.442
AC XY:
32869
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.162
Gnomad4 AMR
AF:
0.550
Gnomad4 ASJ
AF:
0.583
Gnomad4 EAS
AF:
0.683
Gnomad4 SAS
AF:
0.432
Gnomad4 FIN
AF:
0.540
Gnomad4 NFE
AF:
0.541
Gnomad4 OTH
AF:
0.476
Alfa
AF:
0.499
Hom.:
3407
Bravo
AF:
0.433
Asia WGS
AF:
0.532
AC:
1848
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
6.1
DANN
Benign
0.80

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: rs206626; hg19: chr18-10321347; COSMIC: COSV73862170; API