rs17606532

Positions:

• chr16-72299228-G-A

Variant summary

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

The NR_126330.2(LINC01572):​n.690-7815C>T 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 0.0568 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01572	NR_126330.2	n.690-7815C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01572	ENST00000624829.4	n.667-7815C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0144

Gnomad4 AMR AF: 0.0503

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.0440

Gnomad4 FIN AF: 0.0447

Gnomad4 NFE AF: 0.0810

Gnomad4 OTH AF: 0.0572

Alfa AF: 0.0770 Hom.: 403

Bravo AF: 0.0568

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17606532; hg19: chr16-72333127;