19-39237028-G-T

Variant names:

• chr19-39237028-G-T
• rs11673485

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

IFNL3P1 (HGNC:44483): (interferon lambda 3 pseudogene 1)

ENSG00000296032 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 39 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNL3P1		n.39237028G>T		intragenic_variant
LOC124904717	XR_007067256.1	n.321-72C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNL3P1	ENST00000595082.1	n.79-72C>A		intron_variant	Intron 1 of 2	6
ENSG00000296032	ENST00000735578.1	n.116-6208G>T		intron_variant	Intron 1 of 1
ENSG00000296032	ENST00000735579.1	n.90-6208G>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.00375 AC: 89 AN: 23722

American (AMR) AF: 0.00312 AC: 89 AN: 28512

Ashkenazi Jewish (ASJ) AF: 0.00875 AC: 162 AN: 18520

East Asian (EAS) AF: 0.00 AC: 0 AN: 34844

South Asian (SAS) AF: 0.0176 AC: 1092 AN: 61890

European-Finnish (FIN) AF: 0.0467 AC: 1954 AN: 41812

Middle Eastern (MID) AF: 0.00298 AC: 12 AN: 4028

European-Non Finnish (NFE) AF: 0.0254 AC: 18427 AN: 726708

Other (OTH) AF: 0.0182 AC: 800 AN: 43904

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

African (AFR) AF: 0.00443 AC: 184 AN: 41512

American (AMR) AF: 0.00550 AC: 84 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00692 AC: 24 AN: 3470

East Asian (EAS) AF: 0.000582 AC: 3 AN: 5158

South Asian (SAS) AF: 0.0124 AC: 60 AN: 4824

European-Finnish (FIN) AF: 0.0571 AC: 605 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0251 AC: 1705 AN: 67994

Other (OTH) AF: 0.0118 AC: 25 AN: 2114

Alfa AF: 0.0176 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
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs11673485; hg19: chr19-39727668;