chr16-79627600-C-T

Variant names:

• chr16-79627600-C-T
• rs250141
• ENST00000766536.1:n.664-21339G>A

Variant summary

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

The ENST00000766536.1(MAFTRR):​n.664-21339G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,160 control chromosomes in the GnomAD database, including 45,442 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 0.77 (45442 hom., cov: 33)
• Consequence: MAFTRR ENST00000766536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.818 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.664-21339G>A		intron_variant	Intron 9 of 9

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116923 AN: 152042 Hom.: 45410 Cov.: 33

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.769 AC: 117000 AN: 152160 Hom.: 45442 Cov.: 33 AF XY: 0.768 AC XY: 57142 AN XY: 74396

African (AFR) AF: 0.710 AC: 29434 AN: 41472

American (AMR) AF: 0.656 AC: 10026 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2426 AN: 3472

East Asian (EAS) AF: 0.692 AC: 3585 AN: 5180

South Asian (SAS) AF: 0.787 AC: 3793 AN: 4822

European-Finnish (FIN) AF: 0.870 AC: 9220 AN: 10602

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 56009 AN: 68020

Other (OTH) AF: 0.767 AC: 1620 AN: 2112

Alfa AF: 0.750 Hom.: 2655

Bravo AF: 0.745

Asia WGS AF: 0.757 AC: 2634 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.66
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs250141; hg19: chr16-79661497;