rs2250159

Variant names:

• chr9-84162131-T-C
• rs2250159

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.262 AC: 10670 AN: 40718

American (AMR) AF: 0.369 AC: 5600 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1617 AN: 3472

East Asian (EAS) AF: 0.280 AC: 1446 AN: 5170

South Asian (SAS) AF: 0.241 AC: 1164 AN: 4820

European-Finnish (FIN) AF: 0.367 AC: 3866 AN: 10534

Middle Eastern (MID) AF: 0.378 AC: 108 AN: 286

European-Non Finnish (NFE) AF: 0.466 AC: 31607 AN: 67860

Other (OTH) AF: 0.406 AC: 846 AN: 2086

Alfa AF: 0.437 Hom.: 62831

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
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs2250159; hg19: chr9-86777046;