rs7561569

Positions:

• chr2-191154820-C-A

Variant summary

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

The ENST00000623836.1(ENSG00000280083):​n.1251G>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 0.514 in 150,134 control chromosomes in the GnomAD database, including 23,069 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 0.51 (23067 hom., cov: 33)
  • Exomes 𝑓: 0.36 (2 hom.)
• Consequence: ENST00000623836.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAT4	XM_047445600.1	c.27-6616G>T		intron_variant
STAT4	XM_047445601.1	c.27-6616G>T		intron_variant
STAT4	XM_047445602.1	c.27-6616G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000623836.1	n.1251G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77089 AN: 149994 Hom.: 23067 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.526

GnomAD4 exome AF: 0.357 AC: 10 AN: 28 Hom.: 2 Cov.: 0 AF XY: 0.385 AC XY: 10 AN XY: 26

Gnomad4 AFR exome AF: 0.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.514 AC: 77100 AN: 150106 Hom.: 23067 Cov.: 33 AF XY: 0.521 AC XY: 38189 AN XY: 73350

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.523

Alfa AF: 0.538 Hom.: 3596

Bravo AF: 0.497

Asia WGS AF: 0.525 AC: 1821 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7561569; hg19: chr2-192019546;