rs2417226

chr9-101004255-G-Achr9-101004255-G-T

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 0.176 in 151,566 control chromosomes in the GnomAD database, including 2,855 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 (2855 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 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: 0.176 AC: 26683 AN: 151448 Hom.: 2848 Cov.: 30

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.176 AC: 26710 AN: 151566 Hom.: 2855 Cov.: 30 AF XY: 0.184 AC XY: 13604 AN XY: 73990

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.183

Alfa AF: 0.157 Hom.: 416

Bravo AF: 0.169

Asia WGS AF: 0.429 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.22
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2417226; hg19: chr9-103766537;