ENST00000562921.6:n.1638A>G

Variant names:

• chr16-79715456-T-C
• rs3813582
• ENST00000562921.6:n.1638A>G

Variant summary

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

The ENST00000562921.6(MAFTRR):​n.1638A>G 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 0.281 in 152,116 control chromosomes in the GnomAD database, including 6,261 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 0.28 (6261 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MAFTRR ENST00000562921.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.753
• Publications: 33 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371356	XR_001752268.2	n.746+569T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAFTRR	ENST00000562921.6	n.1638A>G		non_coding_transcript_exon_variant	Exon 4 of 4	5
MAFTRR	ENST00000654454.2	n.1799A>G		non_coding_transcript_exon_variant	Exon 5 of 5
MAFTRR	ENST00000658463.1	n.1782A>G		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42724 AN: 151998 Hom.: 6267 Cov.: 33

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.278

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

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) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.281 AC: 42723 AN: 152116 Hom.: 6261 Cov.: 33 AF XY: 0.274 AC XY: 20347 AN XY: 74380

African (AFR) AF: 0.263 AC: 10887 AN: 41466

American (AMR) AF: 0.203 AC: 3104 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1375 AN: 5178

South Asian (SAS) AF: 0.117 AC: 565 AN: 4826

European-Finnish (FIN) AF: 0.300 AC: 3176 AN: 10592

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21581 AN: 67984

Other (OTH) AF: 0.279 AC: 589 AN: 2110

Alfa AF: 0.307 Hom.: 19943

Bravo AF: 0.278

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.41
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs3813582; hg19: chr16-79749353;