16-51768095-A-G

Variant names:

• chr16-51768095-A-G
• rs10163352
• ENST00000563603.3:n.88-3469A>G

Variant summary

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

The ENST00000563603.3(LINC01571):​n.88-3469A>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 ENST00000563603.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 3 publications found

Genes affected

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

LOC105371257 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563603.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01571	NR_110916.1		n.58-3469A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01571	ENST00000563603.3	TSL:2	n.88-3469A>G		intron	N/A
	LINC01571	ENST00000569993.7	TSL:3	n.277-3469A>G		intron	N/A
	LINC01571	ENST00000667113.1		n.134-3469A>G		intron	N/A

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

African (AFR) AF: 0.131 AC: 5453 AN: 41532

American (AMR) AF: 0.248 AC: 3785 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 737 AN: 3468

East Asian (EAS) AF: 0.351 AC: 1812 AN: 5164

South Asian (SAS) AF: 0.355 AC: 1706 AN: 4804

European-Finnish (FIN) AF: 0.362 AC: 3824 AN: 10562

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20368 AN: 67970

Other (OTH) AF: 0.254 AC: 537 AN: 2112

Alfa AF: 0.263 Hom.: 905

Bravo AF: 0.237

Asia WGS AF: 0.344 AC: 1195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.061
DANN	Benign	0.34
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10163352; hg19: chr16-51802006;