16-79715108-C-G

Variant names:

• chr16-79715108-C-G
• rs17767742
• ENST00000561510.5:n.361+221C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000563360.6(LINC01229):​n.508+221C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,018 control chromosomes in the GnomAD database, including 6,129 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 (6129 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LINC01229 ENST00000563360.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.835

Genes affected

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

LOC105371356 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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.746+221C>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01229	ENST00000561510.5	n.361+221C>G		intron_variant	Intron 2 of 5	5
LINC01229	ENST00000563360.6	n.508+221C>G		intron_variant	Intron 3 of 3	4
LINC01229	ENST00000569164.2	n.159+38900C>G		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42197 AN: 151898 Hom.: 6135 Cov.: 33

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.314

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.278 AC: 42194 AN: 152018 Hom.: 6129 Cov.: 33 AF XY: 0.271 AC XY: 20101 AN XY: 74290

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.277

Alfa AF: 0.292 Hom.: 787

Bravo AF: 0.274

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17767742; hg19: chr16-79749005;