ENST00000766536.1:n.663+25054A>G

Variant names:

• chr16-79636427-T-C
• rs728929
• ENST00000766536.1:n.663+25054A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000766536.1(MAFTRR):​n.663+25054A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,648 control chromosomes in the GnomAD database, including 20,632 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 0.51 (20632 hom., cov: 30)
• Consequence: MAFTRR ENST00000766536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAFTRR	ENST00000766536.1	n.663+25054A>G		intron_variant	Intron 9 of 9

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77141 AN: 151530 Hom.: 20619 Cov.: 30

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.509 AC: 77192 AN: 151648 Hom.: 20632 Cov.: 30 AF XY: 0.509 AC XY: 37721 AN XY: 74092

African (AFR) AF: 0.365 AC: 15051 AN: 41292

American (AMR) AF: 0.418 AC: 6367 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1670 AN: 3458

East Asian (EAS) AF: 0.542 AC: 2798 AN: 5160

South Asian (SAS) AF: 0.424 AC: 2024 AN: 4778

European-Finnish (FIN) AF: 0.676 AC: 7086 AN: 10482

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.596 AC: 40470 AN: 67920

Other (OTH) AF: 0.509 AC: 1074 AN: 2112

Alfa AF: 0.557 Hom.: 78781

Bravo AF: 0.482

Asia WGS AF: 0.483 AC: 1676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.75
DANN	Benign	0.45
PhyloP100		-0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs728929; hg19: chr16-79670324;