16-79618644-C-T

Variant names:

• chr16-79618644-C-T
• rs386965
• ENST00000618386.2:n.182-22C>T

Variant summary

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

The ENST00000766536.1(MAFTRR):​n.664-12383G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,110 control chromosomes in the GnomAD database, including 39,305 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 0.71 (39305 hom., cov: 32)
• Consequence: MAFTRR ENST00000766536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.664
• Publications: 17 publications found

Genes affected

ENSG00000275040 (HGNC:):

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.772 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
	ENSG00000275040	ENST00000618386.2	TSL:6	n.182-22C>T		intron	N/A
	MAFTRR	ENST00000766536.1		n.664-12383G>A		intron	N/A
	MAFTRR	ENST00000766575.1		n.343+5818G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108447 AN: 151992 Hom.: 39273 Cov.: 32

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.713 AC: 108527 AN: 152110 Hom.: 39305 Cov.: 32 AF XY: 0.709 AC XY: 52753 AN XY: 74380

African (AFR) AF: 0.663 AC: 27514 AN: 41490

American (AMR) AF: 0.627 AC: 9590 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2829 AN: 3468

East Asian (EAS) AF: 0.470 AC: 2420 AN: 5146

South Asian (SAS) AF: 0.626 AC: 3018 AN: 4820

European-Finnish (FIN) AF: 0.745 AC: 7882 AN: 10584

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52862 AN: 68000

Other (OTH) AF: 0.721 AC: 1522 AN: 2110

Alfa AF: 0.743 Hom.: 77683

Bravo AF: 0.698

Asia WGS AF: 0.588 AC: 2045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.0
DANN	Benign	0.43
PhyloP100		0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs386965;

hg19: chr16-79652541;