chr21-43348682-C-T

Variant names:

• chr21-43348682-C-T
• rs643608

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 0.683 in 152,060 control chromosomes in the GnomAD database, including 35,778 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 0.68 (35778 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103775 AN: 151942 Hom.: 35742 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.683 AC: 103862 AN: 152060 Hom.: 35778 Cov.: 32 AF XY: 0.677 AC XY: 50316 AN XY: 74342

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.666

Alfa AF: 0.676 Hom.: 64696

Bravo AF: 0.682

Asia WGS AF: 0.542 AC: 1885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.98
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs643608; hg19: chr21-44768562;