rs10245440

chr7-21422914-C-A

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 0.273 in 152,088 control chromosomes in the GnomAD database, including 6,164 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 0.27 (6164 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.522 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: 0.273 AC: 41517 AN: 151970 Hom.: 6147 Cov.: 31

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.273 AC: 41581 AN: 152088 Hom.: 6164 Cov.: 31 AF XY: 0.275 AC XY: 20411 AN XY: 74338

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.253

Alfa AF: 0.257 Hom.: 1187

Bravo AF: 0.277

Asia WGS AF: 0.441 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.8
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10245440; hg19: chr7-21462532;