rs2245641

Variant names:

• chr9-15309930-A-C
• rs2245641

Your query was ambiguous. Multiple possible variants found:

• chr9-15309930-A-C
• chr9-15309930-A-G
• chr9-15309930-A-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 0.742 in 152,094 control chromosomes in the GnomAD database, including 42,191 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 0.74 (42191 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

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 (EAS) allele frequency at 95% confidence interval = 0.827 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: 0.742 AC: 112777 AN: 151976 Hom.: 42176 Cov.: 33

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.742 AC: 112834 AN: 152094 Hom.: 42191 Cov.: 33 AF XY: 0.746 AC XY: 55445 AN XY: 74338

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.756

Alfa AF: 0.765 Hom.: 37280

Bravo AF: 0.737

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2245641; hg19: chr9-15309928;