6-151393970-G-A

Variant summary

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

The XM_047419613.1(LOC124901232):​c.*2366G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,672 control chromosomes in the GnomAD database, including 12,908 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 0.37 ( 12908 hom., cov: 30)

Consequence

LOC124901232
XM_047419613.1 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.04
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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124901232XM_047419613.1 linkuse as main transcriptc.*2366G>A 3_prime_UTR_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.374
AC:
56664
AN:
151554
Hom.:
12878
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.614
Gnomad AMI
AF:
0.299
Gnomad AMR
AF:
0.354
Gnomad ASJ
AF:
0.300
Gnomad EAS
AF:
0.690
Gnomad SAS
AF:
0.382
Gnomad FIN
AF:
0.252
Gnomad MID
AF:
0.297
Gnomad NFE
AF:
0.233
Gnomad OTH
AF:
0.355
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.374
AC:
56749
AN:
151672
Hom.:
12908
Cov.:
30
AF XY:
0.377
AC XY:
27944
AN XY:
74098
show subpopulations
Gnomad4 AFR
AF:
0.614
Gnomad4 AMR
AF:
0.354
Gnomad4 ASJ
AF:
0.300
Gnomad4 EAS
AF:
0.689
Gnomad4 SAS
AF:
0.381
Gnomad4 FIN
AF:
0.252
Gnomad4 NFE
AF:
0.233
Gnomad4 OTH
AF:
0.363
Alfa
AF:
0.265
Hom.:
4999
Bravo
AF:
0.395
Asia WGS
AF:
0.551
AC:
1912
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.43
DANN
Benign
0.33

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: rs10002; hg19: chr6-151715105; API