rs4821494

Positions:

• chr22-36482113-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;