21-46622601-G-T

Variant names:

• chr21-46622601-G-T
• rs11910707

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 0.374 in 152,030 control chromosomes in the GnomAD database, including 11,713 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 0.37 (11713 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 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: 0.374 AC: 56812 AN: 151912 Hom.: 11704 Cov.: 33

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.374 AC: 56858 AN: 152030 Hom.: 11713 Cov.: 33 AF XY: 0.375 AC XY: 27891 AN XY: 74310

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.364

Alfa AF: 0.296 Hom.: 6965

Bravo AF: 0.381

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.5
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11910707; hg19: chr21-48042513;