21-26370568-T-C

Position:

• chr21-26370568-T-C

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 0.216 in 152,158 control chromosomes in the GnomAD database, including 3,885 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 0.22 (3885 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 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: 0.216 AC: 32817 AN: 152040 Hom.: 3872 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.216 AC: 32869 AN: 152158 Hom.: 3885 Cov.: 32 AF XY: 0.215 AC XY: 16021 AN XY: 74376

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.0420

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.210

Alfa AF: 0.194 Hom.: 1521

Bravo AF: 0.218

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2830191; hg19: chr21-27742887;