21-46622601-G-T

Variant names:

• chr21-46622601-G-T
• rs11910707

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.548 AC: 22726 AN: 41452

American (AMR) AF: 0.372 AC: 5684 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1070 AN: 3472

East Asian (EAS) AF: 0.139 AC: 721 AN: 5178

South Asian (SAS) AF: 0.302 AC: 1458 AN: 4822

European-Finnish (FIN) AF: 0.365 AC: 3850 AN: 10548

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20101 AN: 67956

Other (OTH) AF: 0.364 AC: 769 AN: 2114

Alfa AF: 0.301 Hom.: 8498

Bravo AF: 0.381

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.5
DANN	Benign	0.45
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs11910707; hg19: chr21-48042513;