Variant chr16-79728170-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000567993.8(MAFTRR):n.413-6549A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,070 control chromosomes in the GnomAD database, including 24,959 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 0.55 ( 24959 hom., cov: 32)

Consequence

MAFTRR
ENST00000567993.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.66

Variant links:

Genes affected

LINC01229 (HGNC:49682): (long intergenic non-protein coding RNA 1229)

LINC01229 links:

MAFTRR (HGNC:51525): (MAF transcriptional regulator RNA)

MAFTRR links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAFTRR	NR_104663.1 link	n.376-6549A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC01229	ENST00000561510.5 link	n.361+13283T>C	intron_variant	5
MAFTRR	ENST00000562921.6 link	n.254-11330A>G	intron_variant	5
MAFTRR	ENST00000567993.8 link	n.413-6549A>G	intron_variant	3

Frequencies

GnomAD3 genomes

AF:

0.551

AC:

83688

AN:

151952

Hom.:

24959

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.705

Gnomad AMR

AF:

0.648

Gnomad ASJ

AF:

0.545

Gnomad EAS

AF:

0.719

Gnomad SAS

AF:

0.579

Gnomad FIN

AF:

0.738

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.633

Gnomad OTH

AF:

0.580

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.550

AC:

83706

AN:

152070

Hom.:

24959

Cov.:

AF XY:

0.558

AC XY:

41481

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.303

Gnomad4 AMR

AF:

0.649

Gnomad4 ASJ

AF:

0.545

Gnomad4 EAS

AF:

0.719

Gnomad4 SAS

AF:

0.579

Gnomad4 FIN

AF:

0.738

Gnomad4 NFE

AF:

0.633

Gnomad4 OTH

AF:

0.574

Alfa

AF:

0.613

Hom.:

27697

Bravo

AF:

0.540

Asia WGS

AF:

0.598

AC:

2081

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.010

DANN

Benign

0.44

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over