16-79728170-T-C

Variant names:

• chr16-79728170-T-C
• rs8056945
• ENST00000561510.5:n.361+13283T>C

Variant summary

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

The ENST00000567993.9(MAFTRR):​n.429-6549A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,070 control chromosomes in the GnomAD database, including 24,959 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 0.55 (24959 hom., cov: 32)
• Consequence: MAFTRR ENST00000567993.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 3 publications found

Genes affected

LINC01229 (HGNC:49682): (long intergenic non-protein coding RNA 1229)

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567993.9. 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
	MAFTRR	NR_104663.1		n.376-6549A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01229	ENST00000561510.5	TSL:5	n.361+13283T>C		intron	N/A
	MAFTRR	ENST00000562921.6	TSL:5	n.254-11330A>G		intron	N/A
	MAFTRR	ENST00000567993.9	TSL:3	n.429-6549A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83688 AN: 151952 Hom.: 24959 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.550 AC: 83706 AN: 152070 Hom.: 24959 Cov.: 32 AF XY: 0.558 AC XY: 41481 AN XY: 74336

African (AFR) AF: 0.303 AC: 12563 AN: 41464

American (AMR) AF: 0.649 AC: 9909 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1890 AN: 3466

East Asian (EAS) AF: 0.719 AC: 3714 AN: 5162

South Asian (SAS) AF: 0.579 AC: 2787 AN: 4814

European-Finnish (FIN) AF: 0.738 AC: 7821 AN: 10594

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43005 AN: 67984

Other (OTH) AF: 0.574 AC: 1212 AN: 2110

Alfa AF: 0.603 Hom.: 35339

Bravo AF: 0.540

Asia WGS AF: 0.598 AC: 2081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.010
DANN	Benign	0.44
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs8056945; hg19: chr16-79762067;