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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371356	XR_001752268.2	n.375-3185C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01229	ENST00000563360.6	n.137-3185C>T		intron_variant	Intron 1 of 3	4
LINC01229	ENST00000569164.2	n.159+34443C>T		intron_variant	Intron 1 of 3	4
LINC01229	ENST00000653222.1	n.150-3185C>T		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs17767419; hg19: chr16-79744548;