21-44985361-C-T

Position:

• chr21-44985361-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 0.216 in 152,160 control chromosomes in the GnomAD database, including 4,309 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 (4309 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 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: 32871 AN: 152042 Hom.: 4307 Cov.: 34

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0582

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.216 AC: 32904 AN: 152160 Hom.: 4309 Cov.: 34 AF XY: 0.213 AC XY: 15841 AN XY: 74378

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0568

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.189

Alfa AF: 0.195 Hom.: 411

Bravo AF: 0.232

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7279521; hg19: chr21-46405276;