chr21-19692305-A-G

Position:

• chr21-19692305-A-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 0.241 in 151,968 control chromosomes in the GnomAD database, including 5,170 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 0.24 (5170 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 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: 0.241 AC: 36592 AN: 151852 Hom.: 5161 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.241 AC: 36644 AN: 151968 Hom.: 5170 Cov.: 32 AF XY: 0.242 AC XY: 17952 AN XY: 74286

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.262

Alfa AF: 0.178 Hom.: 2989

Bravo AF: 0.255

Asia WGS AF: 0.251 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.7
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs218322; hg19: chr21-21064619;