rs2989314

Variant names:

• chr21-20440660-C-A
• rs2989314

Your query was ambiguous. Multiple possible variants found:

• chr21-20440660-C-A
• chr21-20440660-C-T

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 0.0938 in 152,130 control chromosomes in the GnomAD database, including 796 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 0.094 (796 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 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: 0.0939 AC: 14271 AN: 152012 Hom.: 799 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0938 AC: 14274 AN: 152130 Hom.: 796 Cov.: 33 AF XY: 0.0957 AC XY: 7121 AN XY: 74376

African (AFR) AF: 0.119 AC: 4913 AN: 41450

American (AMR) AF: 0.0997 AC: 1524 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3470

East Asian (EAS) AF: 0.163 AC: 842 AN: 5166

South Asian (SAS) AF: 0.0695 AC: 335 AN: 4822

European-Finnish (FIN) AF: 0.116 AC: 1227 AN: 10600

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0707 AC: 4811 AN: 68010

Other (OTH) AF: 0.105 AC: 223 AN: 2114

Alfa AF: 0.0757 Hom.: 867

Bravo AF: 0.0973

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.073
DANN	Benign	0.42
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2989314; hg19: chr21-21812972;