rs3024918

Variant names:

• chr2-191027037-A-G
• rs3024918
• XR_007087796.1:n.2197A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

LOC124900514 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456176.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STAT4-AS1	NR_136318.1		n.31-3848A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STAT4-AS1	ENST00000456176.5	TSL:5	n.31-3848A>G		intron	N/A

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

African (AFR) AF: 0.247 AC: 10272 AN: 41510

American (AMR) AF: 0.281 AC: 4302 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3470

East Asian (EAS) AF: 0.186 AC: 963 AN: 5174

South Asian (SAS) AF: 0.241 AC: 1161 AN: 4820

European-Finnish (FIN) AF: 0.115 AC: 1216 AN: 10612

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11943 AN: 67996

Other (OTH) AF: 0.217 AC: 458 AN: 2114

Alfa AF: 0.195 Hom.: 11419

Bravo AF: 0.225

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.8
DANN	Benign	0.74
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs3024918; hg19: chr2-191891763;