rs7190187

Variant names:

• chr16-79701281-C-T
• rs7190187
• ENST00000563360.6:n.137-12555C>T

Variant summary

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

The ENST00000563360.6(LINC01229):​n.137-12555C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,086 control chromosomes in the GnomAD database, including 6,540 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 (6540 hom., cov: 32)
• Consequence: LINC01229 ENST00000563360.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 10 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.325 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01229	ENST00000563360.6	TSL:4	n.137-12555C>T		intron	N/A
	LINC01229	ENST00000569164.2	TSL:4	n.159+25073C>T		intron	N/A
	LINC01229	ENST00000653222.1		n.150-12555C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43558 AN: 151968 Hom.: 6544 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.286 AC: 43557 AN: 152086 Hom.: 6540 Cov.: 32 AF XY: 0.279 AC XY: 20724 AN XY: 74354

African (AFR) AF: 0.260 AC: 10772 AN: 41482

American (AMR) AF: 0.206 AC: 3154 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 873 AN: 3472

East Asian (EAS) AF: 0.285 AC: 1473 AN: 5166

South Asian (SAS) AF: 0.126 AC: 607 AN: 4820

European-Finnish (FIN) AF: 0.300 AC: 3176 AN: 10570

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.328 AC: 22322 AN: 67980

Other (OTH) AF: 0.279 AC: 590 AN: 2112

Alfa AF: 0.302 Hom.: 859

Bravo AF: 0.283

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7190187;

hg19: chr16-79735178;