rs224869

Variant names:

• chr5-82448142-A-C
• rs224869

Your query was ambiguous. Multiple possible variants found:

• chr5-82448142-A-C
• chr5-82448142-A-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 0.359 in 151,840 control chromosomes in the GnomAD database, including 11,354 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 0.36 (11354 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

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 (SAS) allele frequency at 95% confidence interval = 0.511 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: 0.360 AC: 54559 AN: 151722 Hom.: 11358 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.359 AC: 54555 AN: 151840 Hom.: 11354 Cov.: 31 AF XY: 0.364 AC XY: 27003 AN XY: 74188

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.354

Alfa AF: 0.433 Hom.: 30296

Bravo AF: 0.333

Asia WGS AF: 0.392 AC: 1365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.1
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: rs224869; hg19: chr5-81743961;