16-79736167-A-G

Variant names:

• chr16-79736167-A-G
• rs11646174
• ENST00000561510.5:n.361+21280A>G

Variant summary

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

The ENST00000567993.8(MAFTRR):​n.412+3980T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,028 control chromosomes in the GnomAD database, including 27,001 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 0.58 (27001 hom., cov: 32)
• Consequence: MAFTRR ENST00000567993.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAFTRR	NR_104663.1	n.375+3980T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01229	ENST00000561510.5	n.361+21280A>G		intron_variant	Intron 2 of 5	5
MAFTRR	ENST00000562921.6	n.253+15047T>C		intron_variant	Intron 3 of 3	5
MAFTRR	ENST00000567993.8	n.412+3980T>C		intron_variant	Intron 5 of 5	3

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88896 AN: 151910 Hom.: 26990 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.585 AC: 88936 AN: 152028 Hom.: 27001 Cov.: 32 AF XY: 0.592 AC XY: 43976 AN XY: 74314

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.593

Alfa AF: 0.612 Hom.: 14432

Bravo AF: 0.580

Asia WGS AF: 0.605 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.77
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11646174; hg19: chr16-79770064;