rs9939906

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000624327.1(ENSG00000260664):​n.712-29963A>T 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: ENSG00000260664 ENST00000624327.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.775

Genes affected

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

ENSG00000260664 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.0114

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000470

Gnomad4 OTH AF: 0.0227

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9939906; hg19: chr16-72536895;