rs1837020

Positions:

• chr16-72299677-G-A
• chr16-72299677-G-C

Variant summary

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

The NR_126330.2(LINC01572):​n.690-8264C>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 0.31 in 151,876 control chromosomes in the GnomAD database, including 9,010 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 0.31 (9010 hom., cov: 32)
• Consequence: LINC01572 NR_126330.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01572	NR_126330.2	n.690-8264C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01572	ENST00000624829.4	n.667-8264C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46941 AN: 151758 Hom.: 8962 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.310 AC: 47051 AN: 151876 Hom.: 9010 Cov.: 32 AF XY: 0.314 AC XY: 23280 AN XY: 74238

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.279

Alfa AF: 0.208 Hom.: 4369

Bravo AF: 0.336

Asia WGS AF: 0.414 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1837020; hg19: chr16-72333576;