10-22731421-G-A

Position:

• chr10-22731421-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 0.416 in 151,824 control chromosomes in the GnomAD database, including 16,289 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 (16289 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 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: 0.415 AC: 63012 AN: 151706 Hom.: 16235 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.416 AC: 63114 AN: 151824 Hom.: 16289 Cov.: 32 AF XY: 0.406 AC XY: 30146 AN XY: 74186

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.408

Alfa AF: 0.345 Hom.: 4645

Bravo AF: 0.431

Asia WGS AF: 0.269 AC: 935 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7094187; hg19: chr10-23020350;