rs140174

chr22-23580796-A-G

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 0.449 in 153,562 control chromosomes in the GnomAD database, including 19,445 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 0.45 (19349 hom., cov: 32)
  • Exomes 𝑓: 0.35 (96 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 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: 0.450 AC: 68365 AN: 151962 Hom.: 19297 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.438

GnomAD4 exome AF: 0.349 AC: 516 AN: 1480 Hom.: 96 AF XY: 0.344 AC XY: 269 AN XY: 782

Gnomad4 AFR exome AF: 0.688

Gnomad4 AMR exome AF: 0.473

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.808

Gnomad4 SAS exome AF: 0.526

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.258

Gnomad4 OTH exome AF: 0.352

GnomAD4 genome AF: 0.450 AC: 68478 AN: 152082 Hom.: 19349 Cov.: 32 AF XY: 0.451 AC XY: 33562 AN XY: 74342

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.443

Alfa AF: 0.322 Hom.: 15295

Bravo AF: 0.482

Asia WGS AF: 0.660 AC: 2291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.1
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs140174; hg19: chr22-23922983;