rs198820

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.843G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 1,450,462 control chromosomes in the GnomAD database, including 90,987 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 0.29 ( 7334 hom., cov: 32)
Exomes 𝑓: 0.35 ( 83653 hom. )

Consequence


ENST00000707189.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.90
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=-0.68).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000707189.1 linkuse as main transcriptn.843G>A non_coding_transcript_exon_variant 1/2

Frequencies

GnomAD3 genomes
AF:
0.288
AC:
43699
AN:
151948
Hom.:
7332
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.119
Gnomad AMI
AF:
0.389
Gnomad AMR
AF:
0.311
Gnomad ASJ
AF:
0.308
Gnomad EAS
AF:
0.137
Gnomad SAS
AF:
0.344
Gnomad FIN
AF:
0.361
Gnomad MID
AF:
0.307
Gnomad NFE
AF:
0.379
Gnomad OTH
AF:
0.255
GnomAD4 exome
AF:
0.353
AC:
458968
AN:
1298396
Hom.:
83653
Cov.:
21
AF XY:
0.354
AC XY:
227499
AN XY:
643120
show subpopulations
Gnomad4 AFR exome
AF:
0.104
Gnomad4 AMR exome
AF:
0.329
Gnomad4 ASJ exome
AF:
0.294
Gnomad4 EAS exome
AF:
0.108
Gnomad4 SAS exome
AF:
0.336
Gnomad4 FIN exome
AF:
0.367
Gnomad4 NFE exome
AF:
0.374
Gnomad4 OTH exome
AF:
0.336
GnomAD4 genome
AF:
0.287
AC:
43719
AN:
152066
Hom.:
7334
Cov.:
32
AF XY:
0.286
AC XY:
21254
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.119
Gnomad4 AMR
AF:
0.312
Gnomad4 ASJ
AF:
0.308
Gnomad4 EAS
AF:
0.138
Gnomad4 SAS
AF:
0.346
Gnomad4 FIN
AF:
0.361
Gnomad4 NFE
AF:
0.379
Gnomad4 OTH
AF:
0.258
Alfa
AF:
0.311
Hom.:
761
Bravo
AF:
0.274
Asia WGS
AF:
0.270
AC:
935
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
1.6
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: rs198820; hg19: chr6-26124243; COSMIC: COSV58415959; API