1-152345685-A-G

Position:

• chr1-152345685-A-G

Variant summary

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

The ENST00000445097.2(FLG-AS1):​n.151+4475A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,730 control chromosomes in the GnomAD database, including 6,632 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 0.26 (6632 hom., cov: 32)
• Consequence: FLG-AS1 ENST00000445097.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

FLG-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLG-AS1	NR_103778.1	n.1406+4475A>G		intron_variant
FLG-AS1	NR_103779.1	n.151+4475A>G		intron_variant
FLG-AS1	NR_186761.1	n.1069+4475A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLG-AS1	ENST00000445097.2	n.151+4475A>G		intron_variant		1
FLG-AS1	ENST00000392688.7	n.1406+4475A>G		intron_variant		2
FLG-AS1	ENST00000629331.1	n.61+10246A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.264 AC: 39998 AN: 151612 Hom.: 6610 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.264 AC: 40053 AN: 151730 Hom.: 6632 Cov.: 32 AF XY: 0.268 AC XY: 19881 AN XY: 74178

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.263

Alfa AF: 0.196 Hom.: 723

Bravo AF: 0.285

Asia WGS AF: 0.413 AC: 1434 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.26
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3120667; hg19: chr1-152318161;