16-51768095-A-G

Variant names:

• chr16-51768095-A-G
• rs10163352
• ENST00000569993.6:n.243-3469A>G

Variant summary

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

The ENST00000569993.6(LINC01571):​n.243-3469A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,098 control chromosomes in the GnomAD database, including 5,465 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 (5465 hom., cov: 32)
• Consequence: LINC01571 ENST00000569993.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393

Genes affected

LINC01571 (HGNC:51384): (long intergenic non-protein coding RNA 1571)

LOC105371257 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01571	NR_110916.1	n.58-3469A>G		intron_variant	Intron 1 of 2
LOC105371257	XR_001752182.1	n.84-1442T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01571	ENST00000569993.6	n.243-3469A>G		intron_variant	Intron 1 of 2	3
LINC01571	ENST00000667113.1	n.134-3469A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38611 AN: 151980 Hom.: 5461 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.254 AC: 38626 AN: 152098 Hom.: 5465 Cov.: 32 AF XY: 0.258 AC XY: 19183 AN XY: 74328

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.254

Alfa AF: 0.267 Hom.: 900

Bravo AF: 0.237

Asia WGS AF: 0.344 AC: 1195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.061
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10163352; hg19: chr16-51802006;