rs880290

chr7-140221721-G-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 0.238 in 151,924 control chromosomes in the GnomAD database, including 4,547 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 (4547 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 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: 0.238 AC: 36097 AN: 151806 Hom.: 4546 Cov.: 30

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.238 AC: 36105 AN: 151924 Hom.: 4547 Cov.: 30 AF XY: 0.233 AC XY: 17318 AN XY: 74240

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.0216

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.269

Alfa AF: 0.250 Hom.: 623

Bravo AF: 0.234

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	6.1
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs880290; hg19: chr7-139921521;