rs2250159

Positions:

• chr9-84162131-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 0.38 in 151,028 control chromosomes in the GnomAD database, including 11,494 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 0.38 (11494 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 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: 0.380 AC: 57300 AN: 150916 Hom.: 11490 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.380 AC: 57316 AN: 151028 Hom.: 11494 Cov.: 33 AF XY: 0.371 AC XY: 27367 AN XY: 73800

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.406

Alfa AF: 0.446 Hom.: 31452

Bravo AF: 0.374

Asia WGS AF: 0.270 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2250159; hg19: chr9-86777046;