chr16-72329816-A-G

Position:

• chr16-72329816-A-G

Variant summary

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

The NR_126330.2(LINC01572):​n.689+19251T>C 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 0.0671 in 150,876 control chromosomes in the GnomAD database, including 275 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 0.067 (275 hom., cov: 31)
• Consequence: LINC01572 NR_126330.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

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 = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01572	NR_126330.2	n.689+19251T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01572	ENST00000624829.4	n.666+19251T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0672 AC: 10129 AN: 150750 Hom.: 276 Cov.: 31

Gnomad AFR AF: 0.0402

Gnomad AMI AF: 0.0476

Gnomad AMR AF: 0.0563

Gnomad ASJ AF: 0.0908

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0503

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.0824

Gnomad OTH AF: 0.0649

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

GnomAD4 genome AF: 0.0671 AC: 10123 AN: 150876 Hom.: 275 Cov.: 31 AF XY: 0.0647 AC XY: 4769 AN XY: 73764

Gnomad4 AFR AF: 0.0402

Gnomad4 AMR AF: 0.0562

Gnomad4 ASJ AF: 0.0908

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.0499

Gnomad4 FIN AF: 0.0431

Gnomad4 NFE AF: 0.0824

Gnomad4 OTH AF: 0.0647

Alfa AF: 0.0853 Hom.: 494

Asia WGS AF: 0.0750 AC: 254 AN: 3394

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34522712; hg19: chr16-72363715;