rs17606532

Variant names:

• chr16-72299228-G-A
• rs17606532
• ENST00000624829.4:n.667-7815C>T

Variant summary

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

The NR_126330.2(LINC01572):​n.690-7815C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0568 in 152,164 control chromosomes in the GnomAD database, including 320 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 0.057 (320 hom., cov: 32)
• Consequence: LINC01572 NR_126330.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 3 publications found

Genes affected

LINC01572 (HGNC:51385): (long intergenic non-protein coding RNA 1572)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_126330.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01572	NR_126330.2		n.690-7815C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01572	ENST00000624829.4	TSL:5	n.667-7815C>T		intron	N/A
	LINC01572	ENST00000766023.1		n.708-7815C>T		intron	N/A
	LINC01572	ENST00000766096.1		n.307-7815C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0569 AC: 8647 AN: 152046 Hom.: 321 Cov.: 32

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0503

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.0447

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0810

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0568 AC: 8645 AN: 152164 Hom.: 320 Cov.: 32 AF XY: 0.0548 AC XY: 4076 AN XY: 74382

African (AFR) AF: 0.0144 AC: 597 AN: 41550

American (AMR) AF: 0.0503 AC: 768 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 272 AN: 3468

East Asian (EAS) AF: 0.121 AC: 625 AN: 5146

South Asian (SAS) AF: 0.0440 AC: 212 AN: 4816

European-Finnish (FIN) AF: 0.0447 AC: 474 AN: 10614

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0810 AC: 5503 AN: 67976

Other (OTH) AF: 0.0572 AC: 121 AN: 2114

Alfa AF: 0.0731 Hom.: 486

Bravo AF: 0.0568

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.61
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs17606532; hg19: chr16-72333127;