rs225439

chr21-42311295-G-A

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 0.487 in 150,776 control chromosomes in the GnomAD database, including 18,512 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 0.49 (18512 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

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 (AFR) allele frequency at 95% confidence interval = 0.606 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: 0.487 AC: 73407 AN: 150656 Hom.: 18492 Cov.: 31

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.487 AC: 73476 AN: 150776 Hom.: 18512 Cov.: 31 AF XY: 0.480 AC XY: 35314 AN XY: 73634

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.464

Alfa AF: 0.468 Hom.: 22291

Bravo AF: 0.494

Asia WGS AF: 0.296 AC: 1022 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.040
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225439; hg19: chr21-43731405;