rs2578240

Variant names:

• chr9-88211850-A-G
• rs2578240

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;