21-20440660-C-A

Variant names:

• chr21-20440660-C-A
• rs2989314

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 0.0938 in 152,130 control chromosomes in the GnomAD database, including 796 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 0.094 (796 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 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: 0.0939 AC: 14271 AN: 152012 Hom.: 799 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0938 AC: 14274 AN: 152130 Hom.: 796 Cov.: 33 AF XY: 0.0957 AC XY: 7121 AN XY: 74376

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0997

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.0695

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0729 Hom.: 630

Bravo AF: 0.0973

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.073
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2989314; hg19: chr21-21812972;