rs1574192

Positions:

• chr2-240369088-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 0.263 in 152,114 control chromosomes in the GnomAD database, including 6,600 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 0.26 (6600 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

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 (NFE) allele frequency at 95% confidence interval = 0.377 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: 0.263 AC: 39999 AN: 151996 Hom.: 6603 Cov.: 33

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.263 AC: 39993 AN: 152114 Hom.: 6600 Cov.: 33 AF XY: 0.258 AC XY: 19167 AN XY: 74350

Gnomad4 AFR AF: 0.0947

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.0163

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.279

Alfa AF: 0.343 Hom.: 11236

Bravo AF: 0.246

Asia WGS AF: 0.0870 AC: 304 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	1.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1574192; hg19: chr2-241308505;