16-79736167-A-G

Variant summary

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

The NR_104663.1(MAFTRR):​n.375+3980T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,028 control chromosomes in the GnomAD database, including 27,001 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 0.58 ( 27001 hom., cov: 32)

Consequence

MAFTRR
NR_104663.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.329
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 (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MAFTRRNR_104663.1 linkuse as main transcriptn.375+3980T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC01229ENST00000561510.5 linkuse as main transcriptn.361+21280A>G intron_variant 5
MAFTRRENST00000562921.6 linkuse as main transcriptn.253+15047T>C intron_variant 5
MAFTRRENST00000567993.8 linkuse as main transcriptn.412+3980T>C intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.585
AC:
88896
AN:
151910
Hom.:
26990
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.420
Gnomad AMI
AF:
0.701
Gnomad AMR
AF:
0.677
Gnomad ASJ
AF:
0.545
Gnomad EAS
AF:
0.716
Gnomad SAS
AF:
0.583
Gnomad FIN
AF:
0.737
Gnomad MID
AF:
0.557
Gnomad NFE
AF:
0.632
Gnomad OTH
AF:
0.599
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.585
AC:
88936
AN:
152028
Hom.:
27001
Cov.:
32
AF XY:
0.592
AC XY:
43976
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.419
Gnomad4 AMR
AF:
0.678
Gnomad4 ASJ
AF:
0.545
Gnomad4 EAS
AF:
0.716
Gnomad4 SAS
AF:
0.583
Gnomad4 FIN
AF:
0.737
Gnomad4 NFE
AF:
0.632
Gnomad4 OTH
AF:
0.593
Alfa
AF:
0.612
Hom.:
14432
Bravo
AF:
0.580
Asia WGS
AF:
0.605
AC:
2108
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
0.77
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: rs11646174; hg19: chr16-79770064; API