rs1837020

Variant names:

• chr16-72299677-G-A
• rs1837020
• ENST00000624829.4:n.667-8264C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000624829.4(LINC01572):​n.667-8264C>T variant causes a intron 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 ENST00000624829.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 4 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=-0.92).
• 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 rank	MANE	Protein	UniProt
LINC01572	NR_126330.2	n.690-8264C>T		intron_variant	Intron 9 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01572	ENST00000624829.4	n.667-8264C>T		intron_variant	Intron 9 of 13	5
LINC01572	ENST00000766023.1	n.708-8264C>T		intron_variant	Intron 8 of 12
LINC01572	ENST00000766096.1	n.307-8264C>T		intron_variant	Intron 2 of 6
LINC01572	ENST00000766101.1	n.232-1039C>T		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.490 AC: 20269 AN: 41404

American (AMR) AF: 0.407 AC: 6207 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3468

East Asian (EAS) AF: 0.587 AC: 3011 AN: 5132

South Asian (SAS) AF: 0.244 AC: 1175 AN: 4814

European-Finnish (FIN) AF: 0.233 AC: 2465 AN: 10560

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12627 AN: 67938

Other (OTH) AF: 0.279 AC: 590 AN: 2112

Alfa AF: 0.232 Hom.: 10115

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1837020; hg19: chr16-72333576;