chr21-45019995-G-A

Position:

• chr21-45019995-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 0.0625 in 152,296 control chromosomes in the GnomAD database, including 329 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 0.062 (329 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0971 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: 0.0624 AC: 9501 AN: 152178 Hom.: 328 Cov.: 33

Gnomad AFR AF: 0.0475

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0593

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0801

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0654

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0625 AC: 9513 AN: 152296 Hom.: 329 Cov.: 33 AF XY: 0.0624 AC XY: 4651 AN XY: 74480

Gnomad4 AFR AF: 0.0476

Gnomad4 AMR AF: 0.0591

Gnomad4 ASJ AF: 0.0786

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0806

Gnomad4 FIN AF: 0.0664

Gnomad4 NFE AF: 0.0654

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.0627 Hom.: 52

Bravo AF: 0.0611

Asia WGS AF: 0.106 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36221780; hg19: chr21-46439910;