16-79736167-A-G

Variant names:

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

Variant summary

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

The ENST00000561510.5(LINC01229):​n.361+21280A>G 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: LINC01229 ENST00000561510.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 4 publications found

Genes affected

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

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561510.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAFTRR	NR_104663.1		n.375+3980T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01229	ENST00000561510.5	TSL:5	n.361+21280A>G		intron	N/A
	MAFTRR	ENST00000562921.6	TSL:5	n.253+15047T>C		intron	N/A
	MAFTRR	ENST00000567993.9	TSL:3	n.428+3980T>C		intron	N/A

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

African (AFR) AF: 0.419 AC: 17395 AN: 41468

American (AMR) AF: 0.678 AC: 10360 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1889 AN: 3466

East Asian (EAS) AF: 0.716 AC: 3676 AN: 5132

South Asian (SAS) AF: 0.583 AC: 2815 AN: 4826

European-Finnish (FIN) AF: 0.737 AC: 7786 AN: 10564

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42959 AN: 67974

Other (OTH) AF: 0.593 AC: 1250 AN: 2108

Alfa AF: 0.611 Hom.: 15984

Bravo AF: 0.580

Asia WGS AF: 0.605 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.77
DANN	Benign	0.75
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs11646174; hg19: chr16-79770064;