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. The variant received -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
• Publications: 42 publications found

Genes affected

ENSG00000280087 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623895.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000280087	ENST00000623895.1	TSL:6	n.3847A>G		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AF: 0.500 AC: 2 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 4 AN: 8

South Asian (SAS) AF: 0.333 AC: 2 AN: 6

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.619 AC: 78 AN: 126

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.854 AC: 35406 AN: 41474

American (AMR) AF: 0.503 AC: 7675 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1992 AN: 3468

East Asian (EAS) AF: 0.424 AC: 2172 AN: 5118

South Asian (SAS) AF: 0.443 AC: 2139 AN: 4826

European-Finnish (FIN) AF: 0.730 AC: 7718 AN: 10574

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 42991 AN: 67940

Other (OTH) AF: 0.646 AC: 1361 AN: 2106

Alfa AF: 0.654 Hom.: 36712

Bravo AF: 0.665

Asia WGS AF: 0.543 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.86
DANN	Benign	0.60
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs584007; hg19: chr19-45416478;