rs1422122

Variant names:

• chr5-86077386-A-G
• rs1422122

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 0.319 in 152,006 control chromosomes in the GnomAD database, including 8,093 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 0.32 (8093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48476 AN: 151886 Hom.: 8097 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.319 AC: 48484 AN: 152006 Hom.: 8093 Cov.: 32 AF XY: 0.315 AC XY: 23373 AN XY: 74316

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.323

Alfa AF: 0.350 Hom.: 4780

Bravo AF: 0.320

Asia WGS AF: 0.403 AC: 1403 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1422122; hg19: chr5-85373204;