rs2065306

Positions:

• chr21-38307523-C-G

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 0.101 in 152,034 control chromosomes in the GnomAD database, including 2,166 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 0.10 (2166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

ACMG classification

Verdict is Benign. Variant got -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 = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15249 AN: 151920 Hom.: 2163 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0425

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.0958

Gnomad SAS AF: 0.00580

Gnomad FIN AF: 0.0176

Gnomad MID AF: 0.0513

Gnomad NFE AF: 0.00871

Gnomad OTH AF: 0.0854

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

GnomAD4 genome AF: 0.101 AC: 15286 AN: 152034 Hom.: 2166 Cov.: 32 AF XY: 0.0980 AC XY: 7280 AN XY: 74314

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.0423

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.0961

Gnomad4 SAS AF: 0.00559

Gnomad4 FIN AF: 0.0176

Gnomad4 NFE AF: 0.00871

Gnomad4 OTH AF: 0.0836

Alfa AF: 0.0618 Hom.: 166

Bravo AF: 0.113

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.28
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2065306; hg19: chr21-39679445;