rs17767491

chr16-79711590-A-G

Variant summary

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

The ENST00000661087.1(LINC01229):n.162-2246A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,986 control chromosomes in the GnomAD database, including 5,229 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 0.25 (5229 hom., cov: 32)
• Consequence: LINC01229 ENST00000661087.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

Genes affected

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

LOC105371356 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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/exons	MANE	UniProt
LOC105371356	XR_001752268.2	n.375-2246A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01229	ENST00000661087.1	n.162-2246A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37662 AN: 151866 Hom.: 5236 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.248 AC: 37646 AN: 151986 Hom.: 5229 Cov.: 32 AF XY: 0.242 AC XY: 17971 AN XY: 74280

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.254

Alfa AF: 0.281 Hom.: 1543

Bravo AF: 0.240

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.5
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17767491; hg19: chr16-79745487;