rs1988509

Variant names:

• chr21-44998679-G-A
• rs1988509

Your query was ambiguous. Multiple possible variants found:

• chr21-44998679-G-A
• chr21-44998679-G-C

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 0.373 in 152,110 control chromosomes in the GnomAD database, including 13,148 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 (13148 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 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: 0.373 AC: 56703 AN: 151992 Hom.: 13123 Cov.: 33

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.373 AC: 56783 AN: 152110 Hom.: 13148 Cov.: 33 AF XY: 0.370 AC XY: 27507 AN XY: 74348

African (AFR) AF: 0.659 AC: 27350 AN: 41478

American (AMR) AF: 0.356 AC: 5443 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 862 AN: 3470

East Asian (EAS) AF: 0.329 AC: 1697 AN: 5160

South Asian (SAS) AF: 0.204 AC: 980 AN: 4810

European-Finnish (FIN) AF: 0.246 AC: 2608 AN: 10594

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16778 AN: 67990

Other (OTH) AF: 0.350 AC: 739 AN: 2110

Alfa AF: 0.171 Hom.: 375

Bravo AF: 0.400

Asia WGS AF: 0.298 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.51
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1988509; hg19: chr21-46418593;