2-191026845-G-T

Position:

• chr2-191026845-G-T

Variant summary

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

The XR_007087796.1(LOC124900514):​n.2005G>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 0.207 in 152,212 control chromosomes in the GnomAD database, including 3,492 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 0.21 (3492 hom., cov: 32)
• Consequence: LOC124900514 XR_007087796.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671

Genes affected

LOC124900514 (HGNC:):

STAT4-AS1 (HGNC:55764): (STAT4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900514	XR_007087796.1	n.2005G>T		non_coding_transcript_exon_variant	2/2
STAT4-AS1	NR_136318.1	n.31-4040G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAT4-AS1	ENST00000456176.5	n.31-4040G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31457 AN: 152094 Hom.: 3478 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.207 AC: 31503 AN: 152212 Hom.: 3492 Cov.: 32 AF XY: 0.205 AC XY: 15232 AN XY: 74418

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.215

Alfa AF: 0.0996 Hom.: 150

Bravo AF: 0.224

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.98
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3024919; hg19: chr2-191891571;