rs3813582

Positions:

• chr16-79715456-T-C
• chr16-79715456-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668946.1(MAFTRR):​n.1854A>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 ENST00000668946.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.753

Genes affected

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

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

LOC105371356 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105371356	XR_001752268.2	n.746+569T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAFTRR	ENST00000668946.1	n.1854A>G		non_coding_transcript_exon_variant	6/6
LINC01229	ENST00000661087.1	n.533+569T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.279

Alfa AF: 0.308 Hom.: 6064

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3813582; hg19: chr16-79749353;