rs2069762

chr4-122456825-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 0.256 in 166,840 control chromosomes in the GnomAD database, including 6,559 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 0.25 (5685 hom., cov: 32)
  • Exomes 𝑓: 0.33 (874 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.489 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: 0.248 AC: 37699 AN: 151794 Hom.: 5671 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.297

GnomAD4 exome AF: 0.328 AC: 4903 AN: 14926 Hom.: 874 AF XY: 0.331 AC XY: 2429 AN XY: 7336

Gnomad4 AFR exome AF: 0.0876

Gnomad4 AMR exome AF: 0.318

Gnomad4 ASJ exome AF: 0.452

Gnomad4 EAS exome AF: 0.375

Gnomad4 SAS exome AF: 0.515

Gnomad4 FIN exome AF: 0.343

Gnomad4 NFE exome AF: 0.317

Gnomad4 OTH exome AF: 0.330

GnomAD4 genome AF: 0.248 AC: 37733 AN: 151914 Hom.: 5685 Cov.: 32 AF XY: 0.254 AC XY: 18877 AN XY: 74246

Gnomad4 AFR AF: 0.0737

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.302

Alfa AF: 0.286 Hom.: 3236

Bravo AF: 0.237

Asia WGS AF: 0.422 AC: 1467 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	19
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2069762; hg19: chr4-123377980;