rs584007

chr19-44913221-A-Gchr19-44913221-A-T

Variant summary

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

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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;