16-79646955-G-T

Variant names:

• chr16-79646955-G-T
• rs10514465
• ENST00000766536.1:n.663+14526C>A

Variant summary

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

The ENST00000766536.1(MAFTRR):​n.663+14526C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,064 control chromosomes in the GnomAD database, including 15,003 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 0.43 (15003 hom., cov: 33)
• Consequence: MAFTRR ENST00000766536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAFTRR	ENST00000766536.1	n.663+14526C>A		intron_variant	Intron 9 of 9

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65524 AN: 151946 Hom.: 14997 Cov.: 33

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.434

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.431 AC: 65549 AN: 152064 Hom.: 15003 Cov.: 33 AF XY: 0.430 AC XY: 31982 AN XY: 74358

African (AFR) AF: 0.304 AC: 12603 AN: 41464

American (AMR) AF: 0.377 AC: 5752 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1332 AN: 3468

East Asian (EAS) AF: 0.301 AC: 1556 AN: 5174

South Asian (SAS) AF: 0.331 AC: 1595 AN: 4824

European-Finnish (FIN) AF: 0.589 AC: 6224 AN: 10562

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 35034 AN: 67986

Other (OTH) AF: 0.434 AC: 915 AN: 2106

Alfa AF: 0.398 Hom.: 2819

Bravo AF: 0.407

Asia WGS AF: 0.347 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.19
DANN	Benign	0.23
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs10514465; hg19: chr16-79680852;