16-79648854-T-C

Variant names:

• chr16-79648854-T-C
• rs1424233
• ENST00000766536.1:n.663+12627A>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+12627A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,030 control chromosomes in the GnomAD database, including 15,256 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 0.44 (15256 hom., cov: 33)
• Consequence: MAFTRR ENST00000766536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 78 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 = 0.513 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAFTRR	ENST00000766536.1		n.663+12627A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66208 AN: 151912 Hom.: 15252 Cov.: 33

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.436 AC: 66225 AN: 152030 Hom.: 15256 Cov.: 33 AF XY: 0.435 AC XY: 32284 AN XY: 74298

African (AFR) AF: 0.311 AC: 12911 AN: 41456

American (AMR) AF: 0.380 AC: 5797 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1336 AN: 3466

East Asian (EAS) AF: 0.335 AC: 1730 AN: 5170

South Asian (SAS) AF: 0.328 AC: 1582 AN: 4818

European-Finnish (FIN) AF: 0.590 AC: 6230 AN: 10566

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35169 AN: 67970

Other (OTH) AF: 0.440 AC: 929 AN: 2112

Alfa AF: 0.482 Hom.: 53406

Bravo AF: 0.413

Asia WGS AF: 0.356 AC: 1237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.35
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1424233; hg19: chr16-79682751;