rs36221780

Variant names:

• chr21-45019995-G-A
• rs36221780

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;