chr10-78462711-G-A

Variant summary

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

The ENST00000421324.4(ENSG00000282863):​n.51-66040G>A 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 0.121 in 152,092 control chromosomes in the GnomAD database, including 1,310 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 0.12 ( 1310 hom., cov: 32)

Consequence


ENST00000421324.4 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.981
Variant links:
Genes affected
LINC00595 (HGNC:31430): (long intergenic non-protein coding RNA 595)

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=-0.73).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 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
ENST00000421324.4 linkuse as main transcriptn.51-66040G>A intron_variant, non_coding_transcript_variant 1
LINC00595ENST00000635422.1 linkuse as main transcriptn.63-62619G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.121
AC:
18424
AN:
151974
Hom.:
1305
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0469
Gnomad AMI
AF:
0.104
Gnomad AMR
AF:
0.185
Gnomad ASJ
AF:
0.136
Gnomad EAS
AF:
0.210
Gnomad SAS
AF:
0.113
Gnomad FIN
AF:
0.135
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.144
Gnomad OTH
AF:
0.121
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.121
AC:
18437
AN:
152092
Hom.:
1310
Cov.:
32
AF XY:
0.122
AC XY:
9104
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.0469
Gnomad4 AMR
AF:
0.185
Gnomad4 ASJ
AF:
0.136
Gnomad4 EAS
AF:
0.210
Gnomad4 SAS
AF:
0.113
Gnomad4 FIN
AF:
0.135
Gnomad4 NFE
AF:
0.144
Gnomad4 OTH
AF:
0.122
Alfa
AF:
0.135
Hom.:
357
Bravo
AF:
0.120
Asia WGS
AF:
0.157
AC:
548
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
CADD
Benign
6.8
DANN
Benign
0.95

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: rs10740479; hg19: chr10-80222468; API