21-27455371-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 0.919 in 152,220 control chromosomes in the GnomAD database, including 64,332 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 0.92 (64332 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.918 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: 0.919 AC: 139789 AN: 152102 Hom.: 64288 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.924

Gnomad OTH AF: 0.908

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

GnomAD4 genome AF: 0.919 AC: 139893 AN: 152220 Hom.: 64332 Cov.: 31 AF XY: 0.920 AC XY: 68491 AN XY: 74428

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.852

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.967

Gnomad4 NFE AF: 0.924

Gnomad4 OTH AF: 0.903

Alfa AF: 0.915 Hom.: 82424

Bravo AF: 0.914

Asia WGS AF: 0.888 AC: 3088 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.5
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs242326; hg19: chr21-28827690;