chr16-79612092-C-A

Variant names:

• chr16-79612092-C-A
• rs889472
• ENST00000618386.2:n.181+827C>A

Variant summary

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

The ENST00000618386.2(ENSG00000275040):​n.181+827C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 152,040 control chromosomes in the GnomAD database, including 21,853 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 0.52 (21853 hom., cov: 32)
• Consequence: ENSG00000275040 ENST00000618386.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50
• Publications: 20 publications found

Genes affected

ENSG00000275040 (HGNC:):

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.606 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
ENSG00000275040	ENST00000618386.2	n.181+827C>A		intron_variant	Intron 1 of 1	6
MAFTRR	ENST00000766536.1	n.664-5831G>T		intron_variant	Intron 9 of 9
MAFTRR	ENST00000766575.1	n.344-5831G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79464 AN: 151922 Hom.: 21848 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.523 AC: 79496 AN: 152040 Hom.: 21853 Cov.: 32 AF XY: 0.524 AC XY: 38919 AN XY: 74314

African (AFR) AF: 0.364 AC: 15083 AN: 41468

American (AMR) AF: 0.519 AC: 7922 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1934 AN: 3470

East Asian (EAS) AF: 0.402 AC: 2077 AN: 5166

South Asian (SAS) AF: 0.463 AC: 2229 AN: 4816

European-Finnish (FIN) AF: 0.647 AC: 6832 AN: 10558

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41552 AN: 67980

Other (OTH) AF: 0.545 AC: 1149 AN: 2108

Alfa AF: 0.574 Hom.: 82473

Bravo AF: 0.504

Asia WGS AF: 0.450 AC: 1565 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.031
DANN	Benign	0.27
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs889472; hg19: chr16-79645989;