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. The variant received -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
• Publications: 6 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 (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

African (AFR) AF: 0.644 AC: 26705 AN: 41478

American (AMR) AF: 0.765 AC: 11685 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2610 AN: 3472

East Asian (EAS) AF: 0.848 AC: 4390 AN: 5178

South Asian (SAS) AF: 0.725 AC: 3496 AN: 4820

European-Finnish (FIN) AF: 0.810 AC: 8558 AN: 10564

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52905 AN: 68002

Other (OTH) AF: 0.756 AC: 1593 AN: 2106

Alfa AF: 0.764 Hom.: 46279

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
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs2245641; hg19: chr9-15309928;