chr21-39522634-C-T

Variant names:

• chr21-39522634-C-T
• rs2837066

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 0.145 in 152,068 control chromosomes in the GnomAD database, including 3,238 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 0.15 (3238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 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: 0.145 AC: 22019 AN: 151948 Hom.: 3221 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0601

Gnomad FIN AF: 0.0341

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.0547

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.145 AC: 22072 AN: 152068 Hom.: 3238 Cov.: 32 AF XY: 0.141 AC XY: 10505 AN XY: 74360

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.0868

Gnomad4 ASJ AF: 0.0899

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0595

Gnomad4 FIN AF: 0.0341

Gnomad4 NFE AF: 0.0547

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0794 Hom.: 388

Bravo AF: 0.159

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2837066; hg19: chr21-40894561;