rs2354225

Positions:

• chr19-39557767-G-A

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 0.182 in 152,174 control chromosomes in the GnomAD database, including 3,151 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 0.18 (3151 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.842

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.39557767G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27755 AN: 152056 Hom.: 3152 Cov.: 32

Gnomad AFR AF: 0.0415

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.189

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.182 AC: 27748 AN: 152174 Hom.: 3151 Cov.: 32 AF XY: 0.193 AC XY: 14317 AN XY: 74366

Gnomad4 AFR AF: 0.0413

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.186

Alfa AF: 0.203 Hom.: 594

Bravo AF: 0.166

Asia WGS AF: 0.220 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2354225; hg19: chr19-40048407;