rs445925

Positions:

• chr19-44912383-G-A
• chr19-44912383-G-C

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 0.145 in 152,156 control chromosomes in the GnomAD database, including 2,190 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 0.15 (2189 hom., cov: 32)
  • Exomes 𝑓: 0.069 (1 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22029 AN: 151894 Hom.: 2187 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.126

GnomAD4 exome AF: 0.0694 AC: 10 AN: 144 Hom.: 1 Cov.: 0 AF XY: 0.0510 AC XY: 5 AN XY: 98

Gnomad4 AFR exome AF: 0.333

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0667

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.145 AC: 22058 AN: 152012 Hom.: 2189 Cov.: 32 AF XY: 0.140 AC XY: 10405 AN XY: 74326

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.0729

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.0948

Gnomad4 SAS AF: 0.0642

Gnomad4 FIN AF: 0.0624

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.127

Alfa AF: 0.104 Hom.: 1797

Bravo AF: 0.153

Asia WGS AF: 0.116 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs445925; hg19: chr19-45415640;