rs55925192

chr2-191154393-G-Achr2-191154393-G-C

Variant summary

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

The ENST00000623836.1(ENSG00000280083):n.1678C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,872 control chromosomes in the GnomAD database, including 24,935 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 0.56 (24935 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: ENST00000623836.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

Genes affected

(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 (SAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAT4	XM_047445600.1	c.27-6189C>T		intron_variant
STAT4	XM_047445601.1	c.27-6189C>T		intron_variant
STAT4	XM_047445602.1	c.27-6189C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000623836.1	n.1678C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84392 AN: 151754 Hom.: 24921 Cov.: 31

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.553

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.556 AC: 84451 AN: 151872 Hom.: 24935 Cov.: 31 AF XY: 0.563 AC XY: 41760 AN XY: 74216

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.551

Alfa AF: 0.500 Hom.: 1636

Bravo AF: 0.544

Asia WGS AF: 0.541 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	6.5
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: rs55925192; hg19: chr2-192019119;