8-37597541-G-A

Variant summary

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

The ENST00000519691.1(ENSG00000254290):​n.2318C>T 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 0.451 in 388,260 control chromosomes in the GnomAD database, including 41,194 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 0.42 ( 14180 hom., cov: 33)
Exomes 𝑓: 0.47 ( 27014 hom. )

Consequence


ENST00000519691.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0970
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=-0.82).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC01605NR_170186.1 linkuse as main transcriptn.779+1520C>T intron_variant, non_coding_transcript_variant
LINC01605NR_170187.1 linkuse as main transcriptn.779+1520C>T intron_variant, non_coding_transcript_variant
LINC01605NR_170188.1 linkuse as main transcriptn.779+1520C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000519691.1 linkuse as main transcriptn.2318C>T non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.418
AC:
63589
AN:
151962
Hom.:
14176
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.262
Gnomad AMI
AF:
0.549
Gnomad AMR
AF:
0.471
Gnomad ASJ
AF:
0.390
Gnomad EAS
AF:
0.436
Gnomad SAS
AF:
0.481
Gnomad FIN
AF:
0.552
Gnomad MID
AF:
0.377
Gnomad NFE
AF:
0.475
Gnomad OTH
AF:
0.425
GnomAD4 exome
AF:
0.473
AC:
111631
AN:
236180
Hom.:
27014
Cov.:
0
AF XY:
0.476
AC XY:
62934
AN XY:
132312
show subpopulations
Gnomad4 AFR exome
AF:
0.252
Gnomad4 AMR exome
AF:
0.484
Gnomad4 ASJ exome
AF:
0.400
Gnomad4 EAS exome
AF:
0.441
Gnomad4 SAS exome
AF:
0.491
Gnomad4 FIN exome
AF:
0.551
Gnomad4 NFE exome
AF:
0.477
Gnomad4 OTH exome
AF:
0.462
GnomAD4 genome
AF:
0.418
AC:
63615
AN:
152080
Hom.:
14180
Cov.:
33
AF XY:
0.426
AC XY:
31677
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.261
Gnomad4 AMR
AF:
0.472
Gnomad4 ASJ
AF:
0.390
Gnomad4 EAS
AF:
0.437
Gnomad4 SAS
AF:
0.482
Gnomad4 FIN
AF:
0.552
Gnomad4 NFE
AF:
0.475
Gnomad4 OTH
AF:
0.426
Alfa
AF:
0.447
Hom.:
8825
Bravo
AF:
0.405
Asia WGS
AF:
0.427
AC:
1486
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.7
DANN
Benign
0.75

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: rs2275959; hg19: chr8-37455059; COSMIC: COSV72906546; API