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GeneBe

rs12719740

Variant summary

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

The ENST00000637259.1(ENSG00000293388):n.575-9287C>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 0.208 in 152,014 control chromosomes in the GnomAD database, including 3,386 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 0.21 ( 3386 hom., cov: 32)

Consequence


ENST00000637259.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.649
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=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 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
ENST00000637259.1 linkuse as main transcriptn.575-9287C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.208
AC:
31580
AN:
151896
Hom.:
3383
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.257
Gnomad AMI
AF:
0.170
Gnomad AMR
AF:
0.222
Gnomad ASJ
AF:
0.121
Gnomad EAS
AF:
0.190
Gnomad SAS
AF:
0.197
Gnomad FIN
AF:
0.217
Gnomad MID
AF:
0.168
Gnomad NFE
AF:
0.181
Gnomad OTH
AF:
0.185
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.208
AC:
31597
AN:
152014
Hom.:
3386
Cov.:
32
AF XY:
0.211
AC XY:
15663
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.257
Gnomad4 AMR
AF:
0.222
Gnomad4 ASJ
AF:
0.121
Gnomad4 EAS
AF:
0.189
Gnomad4 SAS
AF:
0.196
Gnomad4 FIN
AF:
0.217
Gnomad4 NFE
AF:
0.181
Gnomad4 OTH
AF:
0.184
Alfa
AF:
0.184
Hom.:
5599
Bravo
AF:
0.211
Asia WGS
AF:
0.215
AC:
746
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
0.38
Dann
Benign
0.67

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: rs12719740; hg19: chr15-99072905; API