rs2578240

Positions:

• chr9-88211850-A-G

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 0.425 in 152,094 control chromosomes in the GnomAD database, including 16,130 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 0.42 (16130 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.869

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64635 AN: 151976 Hom.: 16133 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.425 AC: 64619 AN: 152094 Hom.: 16130 Cov.: 32 AF XY: 0.424 AC XY: 31534 AN XY: 74352

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.494

Alfa AF: 0.542 Hom.: 14003

Bravo AF: 0.403

Asia WGS AF: 0.386 AC: 1342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2578240; hg19: chr9-90826765; COSMIC: COSV60372874;