chr21-38801604-C-T

Variant names:

• chr21-38801604-C-T
• rs1209950

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 0.296 in 152,118 control chromosomes in the GnomAD database, including 7,766 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 0.30 (7766 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 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: 0.296 AC: 45059 AN: 152000 Hom.: 7764 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.0442

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.296 AC: 45064 AN: 152118 Hom.: 7766 Cov.: 33 AF XY: 0.292 AC XY: 21684 AN XY: 74358

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.0441

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.300

Alfa AF: 0.375 Hom.: 21995

Bravo AF: 0.289

Asia WGS AF: 0.107 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	12
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1209950; hg19: chr21-40173528;