rs584007

Variant names:

• chr19-44913221-A-G
• rs584007
• ENST00000623895.1:n.3847A>G

Your query was ambiguous. Multiple possible variants found:

• chr19-44913221-A-G
• chr19-44913221-A-T

Variant summary

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

The ENST00000623895.1(ENSG00000280087):​n.3847A>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 0.672 in 152,132 control chromosomes in the GnomAD database, including 35,687 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 0.67 (35652 hom., cov: 30)
  • Exomes 𝑓: 0.61 (35 hom.)
• Consequence: ENSG00000280087 ENST00000623895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720

Genes affected

ENSG00000280087 (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 (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000280087	ENST00000623895.1	n.3847A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102064 AN: 151860 Hom.: 35593 Cov.: 30

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.642

GnomAD4 exome AF: 0.610 AC: 94 AN: 154 Hom.: 35 Cov.: 0 AF XY: 0.597 AC XY: 74 AN XY: 124

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.619

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.672 AC: 102191 AN: 151978 Hom.: 35652 Cov.: 30 AF XY: 0.669 AC XY: 49716 AN XY: 74296

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.646

Alfa AF: 0.636 Hom.: 25444

Bravo AF: 0.665

Asia WGS AF: 0.543 AC: 1892 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	0.86
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs584007; hg19: chr19-45416478;