chr16-72502996-A-T

Variant names:

• chr16-72502996-A-T
• rs9939906
• ENST00000561611.2:n.114-23206T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000561611.2(LINC01572):​n.114-23206T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0304 in 152,222 control chromosomes in the GnomAD database, including 239 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 0.030 (239 hom., cov: 32)
• Consequence: LINC01572 ENST00000561611.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.775
• Publications: 2 publications found

Genes affected

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

ENSG00000260664 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01572	NR_126330.2	n.411+19557T>A		intron_variant	Intron 6 of 13
LINC01572	NR_159371.1	n.197+20336T>A		intron_variant	Intron 3 of 5
LINC01572	NR_159372.1	n.349+19557T>A		intron_variant	Intron 5 of 7
LOC124903718	XR_007065114.1	n.4119-29963A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01572	ENST00000561611.2	n.114-23206T>A		intron_variant	Intron 1 of 2	3
LINC01572	ENST00000563770.5	n.466-11030T>A		intron_variant	Intron 6 of 7	5
ENSG00000260664	ENST00000624327.1	n.712-29963A>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0304 AC: 4624 AN: 152104 Hom.: 239 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0115

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000470

Gnomad OTH AF: 0.0229

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

GnomAD4 genome AF: 0.0304 AC: 4635 AN: 152222 Hom.: 239 Cov.: 32 AF XY: 0.0299 AC XY: 2223 AN XY: 74434

African (AFR) AF: 0.105 AC: 4372 AN: 41510

American (AMR) AF: 0.0114 AC: 175 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00 AC: 0 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000470 AC: 32 AN: 68018

Other (OTH) AF: 0.0227 AC: 48 AN: 2114

Alfa AF: 0.0237 Hom.: 16

Bravo AF: 0.0344

Asia WGS AF: 0.00491 AC: 17 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	16
DANN	Benign	0.80
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs9939906; hg19: chr16-72536895;