chr21-44989526-G-A

Variant names:

• chr21-44989526-G-A
• rs11701193

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 0.527 in 152,126 control chromosomes in the GnomAD database, including 21,986 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 0.53 (21986 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.684 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: 0.527 AC: 80171 AN: 152008 Hom.: 21983 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.527 AC: 80209 AN: 152126 Hom.: 21986 Cov.: 33 AF XY: 0.531 AC XY: 39458 AN XY: 74356

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.546

Alfa AF: 0.557 Hom.: 4033

Bravo AF: 0.509

Asia WGS AF: 0.656 AC: 2278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11701193; hg19: chr21-46409441;