rs4821494

Variant names:

• chr22-36482113-G-T
• rs4821494

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 0.583 in 148,838 control chromosomes in the GnomAD database, including 27,173 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 0.58 (27166 hom., cov: 22)
  • Exomes 𝑓: 0.52 (7 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 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: 0.583 AC: 86692 AN: 148684 Hom.: 27159 Cov.: 22

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.619

GnomAD4 exome AF: 0.522 AC: 24 AN: 46 Hom.: 7 AF XY: 0.474 AC XY: 18 AN XY: 38

Gnomad4 SAS exome AF: 0.412

Gnomad4 NFE exome AF: 0.833

GnomAD4 genome AF: 0.583 AC: 86724 AN: 148792 Hom.: 27166 Cov.: 22 AF XY: 0.575 AC XY: 41660 AN XY: 72470

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.615

Alfa AF: 0.624 Hom.: 4435

Bravo AF: 0.585

Asia WGS AF: 0.327 AC: 1138 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4821494; hg19: chr22-36878160;