chr16-79701090-G-A

Variant names:

• chr16-79701090-G-A
• rs7188445
• ENST00000563360.6:n.137-12746G>A

Variant summary

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

The ENST00000563360.6(LINC01229):​n.137-12746G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,728 control chromosomes in the GnomAD database, including 6,549 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 0.29 (6549 hom., cov: 31)
• Consequence: LINC01229 ENST00000563360.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 42 publications found

Genes affected

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

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

LOC105371356 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563360.6. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01229	ENST00000563360.6	TSL:4	n.137-12746G>A		intron	N/A
	LINC01229	ENST00000569164.2	TSL:4	n.159+24882G>A		intron	N/A
	LINC01229	ENST00000653222.1		n.150-12746G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43636 AN: 151610 Hom.: 6554 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.288 AC: 43635 AN: 151728 Hom.: 6549 Cov.: 31 AF XY: 0.280 AC XY: 20747 AN XY: 74120

African (AFR) AF: 0.261 AC: 10789 AN: 41348

American (AMR) AF: 0.208 AC: 3183 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3466

East Asian (EAS) AF: 0.288 AC: 1479 AN: 5134

South Asian (SAS) AF: 0.129 AC: 620 AN: 4820

European-Finnish (FIN) AF: 0.300 AC: 3151 AN: 10486

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22343 AN: 67888

Other (OTH) AF: 0.282 AC: 594 AN: 2106

Alfa AF: 0.297 Hom.: 2012

Bravo AF: 0.284

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.83
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs7188445; hg19: chr16-79734987;