19-3626924-T-C

Position:

• chr19-3626924-T-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 0.636 in 607,984 control chromosomes in the GnomAD database, including 124,511 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 0.68 (35447 hom., cov: 36)
  • Exomes 𝑓: 0.62 (89064 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.3626924T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.677 AC: 103048 AN: 152130 Hom.: 35408 Cov.: 36

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.682

GnomAD4 exome AF: 0.622 AC: 283329 AN: 455736 Hom.: 89064 AF XY: 0.621 AC XY: 142241 AN XY: 229106

Gnomad4 AFR exome AF: 0.794

Gnomad4 AMR exome AF: 0.706

Gnomad4 ASJ exome AF: 0.653

Gnomad4 EAS exome AF: 0.589

Gnomad4 SAS exome AF: 0.590

Gnomad4 FIN exome AF: 0.656

Gnomad4 NFE exome AF: 0.613

Gnomad4 OTH exome AF: 0.642

GnomAD4 genome AF: 0.677 AC: 103140 AN: 152248 Hom.: 35447 Cov.: 36 AF XY: 0.678 AC XY: 50437 AN XY: 74428

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.676

Alfa AF: 0.635 Hom.: 50887

Bravo AF: 0.687

Asia WGS AF: 0.602 AC: 2095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2271875; hg19: chr19-3626922;