16-79666550-G-C

Variant names:

• chr16-79666550-G-C
• rs4889009
• ENST00000766536.1:n.543+1121C>G

Variant summary

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

The ENST00000766536.1(MAFTRR):​n.543+1121C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,980 control chromosomes in the GnomAD database, including 26,618 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 0.59 (26618 hom., cov: 32)
• Consequence: MAFTRR ENST00000766536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 9 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.687 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAFTRR	ENST00000766536.1		n.543+1121C>G		intron	N/A
	MAFTRR	ENST00000766537.1		n.541+1121C>G		intron	N/A
	MAFTRR	ENST00000766538.1		n.540+1121C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89051 AN: 151862 Hom.: 26605 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.586 AC: 89097 AN: 151980 Hom.: 26618 Cov.: 32 AF XY: 0.591 AC XY: 43929 AN XY: 74288

African (AFR) AF: 0.502 AC: 20805 AN: 41418

American (AMR) AF: 0.627 AC: 9574 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2448 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1971 AN: 5156

South Asian (SAS) AF: 0.707 AC: 3408 AN: 4822

European-Finnish (FIN) AF: 0.672 AC: 7101 AN: 10564

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41946 AN: 67978

Other (OTH) AF: 0.592 AC: 1243 AN: 2098

Alfa AF: 0.467 Hom.: 1280

Bravo AF: 0.577

Asia WGS AF: 0.517 AC: 1801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.61
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs4889009; hg19: chr16-79700447;