rs2989314

chr21-20440660-C-Achr21-20440660-C-T

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 0.0938 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0997

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.0695

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0729 Hom.: 630

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2989314; hg19: chr21-21812972;