rs422858

chr3-148697697-A-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 0.2 in 152,068 control chromosomes in the GnomAD database, including 3,275 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 0.20 (3275 hom., cov: 32)
  • Exomes 𝑓: 0.083 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 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: 0.200 AC: 30373 AN: 151952 Hom.: 3264 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.216

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0833 AC: 1 AN: 12 Hom.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.167

GnomAD4 genome AF: 0.200 AC: 30408 AN: 152068 Hom.: 3275 Cov.: 32 AF XY: 0.198 AC XY: 14700 AN XY: 74350

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.214

Alfa AF: 0.206 Hom.: 302

Bravo AF: 0.201

Asia WGS AF: 0.146 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	9.9
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs422858; hg19: chr3-148415484;