rs3813582

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000654454.2(MAFTRR):​n.1799A>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 ENST00000654454.2 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654454.2. 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.1638A>G		non_coding_transcript_exon	Exon 4 of 4
	MAFTRR	ENST00000654454.2		n.1799A>G		non_coding_transcript_exon	Exon 5 of 5
	MAFTRR	ENST00000658463.1		n.1782A>G		non_coding_transcript_exon	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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3813582;

hg19: chr16-79749353;