rs11590365

Variant names:

• chr1-152193013-C-A
• rs11590365
• ENST00000420707.5:n.158+3505C>A

Variant summary

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

The ENST00000593011.5(FLG-AS1):​n.296+24593C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,064 control chromosomes in the GnomAD database, including 3,124 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 0.16 (3124 hom., cov: 32)
• Consequence: FLG-AS1 ENST00000593011.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

Genes affected

FLG-AS1 (HGNC:):

PUDPP2 (HGNC:20195): (pseudouridine 5'-phosphatase pseudogene 2)

CCDST (HGNC:55988): (cervical cancer associated DHX9 suppressive transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDST	NR_186761.1	n.353+3358C>A		intron_variant	Intron 1 of 7
CCDST	NR_186762.1	n.179+3532C>A		intron_variant	Intron 1 of 5
CCDST	NR_186763.1	n.206+3505C>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLG-AS1	ENST00000420707.5	n.158+3505C>A		intron_variant	Intron 1 of 8	5
FLG-AS1	ENST00000593011.5	n.296+24593C>A		intron_variant	Intron 1 of 3	4
PUDPP2	ENST00000628080.1	n.47+3640G>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23871 AN: 151948 Hom.: 3121 Cov.: 32

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.157 AC: 23870 AN: 152064 Hom.: 3124 Cov.: 32 AF XY: 0.168 AC XY: 12520 AN XY: 74332

Gnomad4 AFR AF: 0.0369

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.190

Alfa AF: 0.152 Hom.: 1025

Bravo AF: 0.166

Asia WGS AF: 0.445 AC: 1548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11590365; hg19: chr1-152165489;