ENST00000562921.6:n.1715C>T

Variant names:

• chr16-79715379-G-A
• rs3813579
• ENST00000562921.6:n.1715C>T

Variant summary

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

The ENST00000562921.6(MAFTRR):​n.1715C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,834 control chromosomes in the GnomAD database, including 17,839 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 0.48 (17839 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: MAFTRR ENST00000562921.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373
• Publications: 22 publications found

Genes affected

MAFTRR (HGNC:51525): (MAF transcriptional regulator RNA)

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

LOC105371356 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562921.6. 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
	MAFTRR	ENST00000562921.6	TSL:5	n.1715C>T		non_coding_transcript_exon	Exon 4 of 4
	MAFTRR	ENST00000654454.2		n.1876C>T		non_coding_transcript_exon	Exon 5 of 5
	MAFTRR	ENST00000658463.1		n.1859C>T		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72807 AN: 151716 Hom.: 17846 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.473

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.480 AC: 72809 AN: 151834 Hom.: 17839 Cov.: 32 AF XY: 0.478 AC XY: 35443 AN XY: 74208

African (AFR) AF: 0.369 AC: 15263 AN: 41364

American (AMR) AF: 0.467 AC: 7130 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1459 AN: 3470

East Asian (EAS) AF: 0.574 AC: 2967 AN: 5166

South Asian (SAS) AF: 0.452 AC: 2178 AN: 4818

European-Finnish (FIN) AF: 0.546 AC: 5745 AN: 10520

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.534 AC: 36282 AN: 67922

Other (OTH) AF: 0.472 AC: 995 AN: 2110

Alfa AF: 0.517 Hom.: 73284

Bravo AF: 0.475

Asia WGS AF: 0.449 AC: 1563 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.57
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs3813579; hg19: chr16-79749276;