19-39237028-G-T

Position:

• chr19-39237028-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0223 in 1,136,098 control chromosomes in the GnomAD database, including 412 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 0.018 (39 hom., cov: 31)
  • Exomes 𝑓: 0.023 (373 hom.)
• Consequence: IFNL3P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376

Genes affected

IFNL3P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0178 (2715/152158) while in subpopulation NFE AF= 0.0251 (1705/67994). AF 95% confidence interval is 0.0241. There are 39 homozygotes in gnomad4. There are 1422 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 39 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFNL3P1		n.39237028G>T		intragenic_variant
LOC124904717	XR_007067256.1	n.321-72C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNL3P1	ENST00000595082.1	n.79-72C>A		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.0179 AC: 2715 AN: 152040 Hom.: 39 Cov.: 31

Gnomad AFR AF: 0.00445

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.00551

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.000580

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.0571

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0251

Gnomad OTH AF: 0.0120

GnomAD4 exome AF: 0.0230 AC: 22625 AN: 983940 Hom.: 373 Cov.: 13 AF XY: 0.0229 AC XY: 11339 AN XY: 495302

Gnomad4 AFR exome AF: 0.00375

Gnomad4 AMR exome AF: 0.00312

Gnomad4 ASJ exome AF: 0.00875

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0176

Gnomad4 FIN exome AF: 0.0467

Gnomad4 NFE exome AF: 0.0254

Gnomad4 OTH exome AF: 0.0182

GnomAD4 genome AF: 0.0178 AC: 2715 AN: 152158 Hom.: 39 Cov.: 31 AF XY: 0.0191 AC XY: 1422 AN XY: 74378

Gnomad4 AFR AF: 0.00443

Gnomad4 AMR AF: 0.00550

Gnomad4 ASJ AF: 0.00692

Gnomad4 EAS AF: 0.000582

Gnomad4 SAS AF: 0.0124

Gnomad4 FIN AF: 0.0571

Gnomad4 NFE AF: 0.0251

Gnomad4 OTH AF: 0.0118

Alfa AF: 0.0182 Hom.: 4

Bravo AF: 0.0137

Asia WGS AF: 0.00318 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.20
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11673485; hg19: chr19-39727668;