19-34791150-C-T

Variant names:

• chr19-34791150-C-T
• rs11084785
• ENST00000587150.3:n.1361+670G>A

Variant summary

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

The ENST00000587150.3(LINC01801):​n.1361+670G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,988 control chromosomes in the GnomAD database, including 11,012 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 0.37 (11012 hom., cov: 32)
• Consequence: LINC01801 ENST00000587150.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 4 publications found

Genes affected

LINC01801 (HGNC:52592): (long intergenic non-protein coding RNA 1801)

ZNF599 (HGNC:26408): (zinc finger protein 599) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF599	XM_047438254.1	c.-512+670G>A		intron_variant	Intron 3 of 7		XP_047294210.1
ZNF599	XM_047438255.1	c.-566+670G>A		intron_variant	Intron 5 of 10		XP_047294211.1
ZNF599	XM_047438256.1	c.-566+670G>A		intron_variant	Intron 4 of 9		XP_047294212.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01801	ENST00000587150.3	n.1361+670G>A		intron_variant	Intron 4 of 4	5
LINC01801	ENST00000654750.1	n.484+670G>A		intron_variant	Intron 4 of 4
LINC01801	ENST00000715855.1	n.1300+670G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56526 AN: 151870 Hom.: 11010 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.372 AC: 56543 AN: 151988 Hom.: 11012 Cov.: 32 AF XY: 0.369 AC XY: 27382 AN XY: 74270

African (AFR) AF: 0.286 AC: 11840 AN: 41436

American (AMR) AF: 0.376 AC: 5752 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1676 AN: 3466

East Asian (EAS) AF: 0.138 AC: 714 AN: 5164

South Asian (SAS) AF: 0.308 AC: 1480 AN: 4810

European-Finnish (FIN) AF: 0.447 AC: 4718 AN: 10560

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.429 AC: 29151 AN: 67962

Other (OTH) AF: 0.408 AC: 861 AN: 2108

Alfa AF: 0.400 Hom.: 9495

Bravo AF: 0.365

Asia WGS AF: 0.238 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.38
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs11084785; hg19: chr19-35282054;