chr21-38801604-C-T

Position:

• chr21-38801604-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 0.296 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;