rs10239907

chr7-25092760-G-Achr7-25092760-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 0.219 in 151,570 control chromosomes in the GnomAD database, including 3,769 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 0.22 (3769 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33125 AN: 151466 Hom.: 3766 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.219 AC: 33141 AN: 151570 Hom.: 3769 Cov.: 31 AF XY: 0.222 AC XY: 16440 AN XY: 74044

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.213

Alfa AF: 0.229 Hom.: 6978

Bravo AF: 0.214

Asia WGS AF: 0.228 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.2
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10239907; hg19: chr7-25132379; COSMIC: COSV70884489;