rs17767419

Variant names:

• chr16-79710651-C-T
• rs17767419
• ENST00000563360.6:n.137-3185C>T

Variant summary

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

The ENST00000563360.6(LINC01229):​n.137-3185C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,062 control chromosomes in the GnomAD database, including 6,198 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 0.28 (6198 hom., cov: 32)
• Consequence: LINC01229 ENST00000563360.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 25 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 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.137-3185C>T		intron	N/A
	LINC01229	ENST00000569164.2	TSL:4	n.159+34443C>T		intron	N/A
	LINC01229	ENST00000653222.1		n.150-3185C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42496 AN: 151944 Hom.: 6205 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.279 AC: 42489 AN: 152062 Hom.: 6198 Cov.: 32 AF XY: 0.272 AC XY: 20239 AN XY: 74334

African (AFR) AF: 0.257 AC: 10658 AN: 41474

American (AMR) AF: 0.204 AC: 3111 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3468

East Asian (EAS) AF: 0.267 AC: 1378 AN: 5170

South Asian (SAS) AF: 0.117 AC: 564 AN: 4824

European-Finnish (FIN) AF: 0.301 AC: 3179 AN: 10556

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21570 AN: 67976

Other (OTH) AF: 0.277 AC: 583 AN: 2108

Alfa AF: 0.305 Hom.: 21651

Bravo AF: 0.276

Asia WGS AF: 0.172 AC: 598 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.58
PhyloP100		0.070

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: rs17767419;

hg19: chr16-79744548;