rs3813579

chr16-79715379-G-Achr16-79715379-G-Cchr16-79715379-G-T

Variant summary

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

The ENST00000668946.1(MAFTRR):n.1931C>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 ENST00000668946.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371356	XR_001752268.2	n.746+492G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAFTRR	ENST00000668946.1	n.1931C>T		non_coding_transcript_exon_variant	6/6
LINC01229	ENST00000661087.1	n.533+492G>A		intron_variant, non_coding_transcript_variant

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

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

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.472

Alfa AF: 0.524 Hom.: 30159

Bravo AF: 0.475

Asia WGS AF: 0.449 AC: 1563 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.35
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3813579; hg19: chr16-79749276;