rs34522712

Variant names:

• chr16-72329816-A-G
• rs34522712
• ENST00000624829.4:n.666+19251T>C

Variant summary

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

The NR_126330.2(LINC01572):​n.689+19251T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 2 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 = 0.158 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.689+19251T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01572	ENST00000624829.4	TSL:5	n.666+19251T>C		intron	N/A
	LINC01572	ENST00000766023.1		n.707+19230T>C		intron	N/A
	LINC01572	ENST00000766096.1		n.306+19230T>C		intron	N/A

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

African (AFR) AF: 0.0402 AC: 1658 AN: 41288

American (AMR) AF: 0.0562 AC: 853 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.0908 AC: 312 AN: 3438

East Asian (EAS) AF: 0.168 AC: 843 AN: 5032

South Asian (SAS) AF: 0.0499 AC: 236 AN: 4730

European-Finnish (FIN) AF: 0.0431 AC: 452 AN: 10488

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.0824 AC: 5556 AN: 67450

Other (OTH) AF: 0.0647 AC: 135 AN: 2088

Alfa AF: 0.0827 Hom.: 586

Asia WGS AF: 0.0750 AC: 254 AN: 3394

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.25
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs34522712; hg19: chr16-72363715;