rs3024918

Positions:

• chr2-191027037-A-G

Variant summary

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

The XR_007087796.1(LOC124900514):​n.2197A>G 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 0.208 in 152,192 control chromosomes in the GnomAD database, including 3,528 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 (3528 hom., cov: 32)
• Consequence: LOC124900514 XR_007087796.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543

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=-0.96).
• 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.2197A>G		non_coding_transcript_exon_variant	2/2
STAT4-AS1	NR_136318.1	n.31-3848A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAT4-AS1	ENST00000456176.5	n.31-3848A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31608 AN: 152074 Hom.: 3514 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.208 AC: 31654 AN: 152192 Hom.: 3528 Cov.: 32 AF XY: 0.206 AC XY: 15301 AN XY: 74418

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.217

Alfa AF: 0.194 Hom.: 5126

Bravo AF: 0.225

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	-0.96
CADD	Benign	2.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3024918; hg19: chr2-191891763;