chr16-79715379-G-A

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371356	XR_001752268.2	n.746+492G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAFTRR	ENST00000562921.6	n.1715C>T		non_coding_transcript_exon_variant	Exon 4 of 4	5
MAFTRR	ENST00000654454.2	n.1876C>T		non_coding_transcript_exon_variant	Exon 5 of 5
MAFTRR	ENST00000658463.1	n.1859C>T		non_coding_transcript_exon_variant	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 v4.3

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;