21-23770802-G-A

Position:

• chr21-23770802-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 0.668 in 151,962 control chromosomes in the GnomAD database, including 34,271 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 0.67 (34271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101499 AN: 151844 Hom.: 34238 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.668 AC: 101575 AN: 151962 Hom.: 34271 Cov.: 32 AF XY: 0.675 AC XY: 50129 AN XY: 74266

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.665

Alfa AF: 0.673 Hom.: 79049

Bravo AF: 0.667

Asia WGS AF: 0.758 AC: 2635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2828520; hg19: chr21-25143119;