chr6-14988536-T-C

Variant summary

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

The ENST00000437648.1(ENSG00000234261):​n.486+8880A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,916 control chromosomes in the GnomAD database, including 13,246 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 0.40 ( 13246 hom., cov: 31)

Consequence

ENSG00000234261
ENST00000437648.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.78
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=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC105374945XR_007059473.1 linkn.220+8880A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000234261ENST00000437648.1 linkn.486+8880A>G intron_variant 5
ENSG00000234261ENST00000629853.2 linkn.204+8880A>G intron_variant 5
ENSG00000234261ENST00000653525.1 linkn.397+8880A>G intron_variant

Frequencies

GnomAD3 genomes
AF:
0.395
AC:
59980
AN:
151796
Hom.:
13204
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.597
Gnomad AMI
AF:
0.438
Gnomad AMR
AF:
0.351
Gnomad ASJ
AF:
0.405
Gnomad EAS
AF:
0.330
Gnomad SAS
AF:
0.596
Gnomad FIN
AF:
0.297
Gnomad MID
AF:
0.303
Gnomad NFE
AF:
0.289
Gnomad OTH
AF:
0.375
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.395
AC:
60082
AN:
151916
Hom.:
13246
Cov.:
31
AF XY:
0.398
AC XY:
29556
AN XY:
74260
show subpopulations
Gnomad4 AFR
AF:
0.597
Gnomad4 AMR
AF:
0.351
Gnomad4 ASJ
AF:
0.405
Gnomad4 EAS
AF:
0.330
Gnomad4 SAS
AF:
0.597
Gnomad4 FIN
AF:
0.297
Gnomad4 NFE
AF:
0.289
Gnomad4 OTH
AF:
0.377
Alfa
AF:
0.311
Hom.:
16125
Bravo
AF:
0.400
Asia WGS
AF:
0.491
AC:
1706
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.33
DANN
Benign
0.49

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: rs2327869; hg19: chr6-14988767; API