chr21-44983435-G-T

Position:

• chr21-44983435-G-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 0.146 in 152,036 control chromosomes in the GnomAD database, including 1,741 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 0.15 (1741 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.204 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: 0.147 AC: 22263 AN: 151918 Hom.: 1744 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.146 AC: 22264 AN: 152036 Hom.: 1741 Cov.: 33 AF XY: 0.147 AC XY: 10940 AN XY: 74296

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0565

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.129

Alfa AF: 0.156 Hom.: 225

Bravo AF: 0.152

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.12
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs928308; hg19: chr21-46403350;