ENST00000766536.1:n.663+6451G>A

Variant names:

• chr16-79655030-C-T
• rs8048408
• ENST00000766536.1:n.663+6451G>A

Variant summary

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

The ENST00000766536.1(MAFTRR):​n.663+6451G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,012 control chromosomes in the GnomAD database, including 14,397 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 0.42 (14397 hom., cov: 32)
• Consequence: MAFTRR ENST00000766536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766536.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAFTRR	ENST00000766536.1		n.663+6451G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63727 AN: 151894 Hom.: 14397 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.419 AC: 63740 AN: 152012 Hom.: 14397 Cov.: 32 AF XY: 0.420 AC XY: 31193 AN XY: 74302

African (AFR) AF: 0.262 AC: 10870 AN: 41464

American (AMR) AF: 0.372 AC: 5672 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1357 AN: 3468

East Asian (EAS) AF: 0.406 AC: 2088 AN: 5146

South Asian (SAS) AF: 0.310 AC: 1492 AN: 4820

European-Finnish (FIN) AF: 0.592 AC: 6250 AN: 10564

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34580 AN: 67968

Other (OTH) AF: 0.426 AC: 901 AN: 2114

Alfa AF: 0.468 Hom.: 23331

Bravo AF: 0.396

Asia WGS AF: 0.374 AC: 1299 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.74
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs8048408; hg19: chr16-79688927;