rs4907240

Positions:

• chr2-96562302-G-A
• chr2-96562302-G-C

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 0.239 in 152,124 control chromosomes in the GnomAD database, including 5,874 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 0.24 (5874 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.627 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: 0.239 AC: 36327 AN: 152006 Hom.: 5859 Cov.: 32

Gnomad AFR AF: 0.0744

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.239 AC: 36359 AN: 152124 Hom.: 5874 Cov.: 32 AF XY: 0.245 AC XY: 18210 AN XY: 74366

Gnomad4 AFR AF: 0.0744

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.295

Alfa AF: 0.270 Hom.: 7107

Bravo AF: 0.245

Asia WGS AF: 0.541 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4907240; hg19: chr2-97228039;