rs7283476

chr21-30243783-A-Tchr21-30243783-A-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 0.0611 in 151,994 control chromosomes in the GnomAD database, including 435 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 0.061 (435 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

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 (AFR) allele frequency at 95% confidence interval = 0.124 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: 0.0610 AC: 9266 AN: 151874 Hom.: 430 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0263

Gnomad EAS AF: 0.00675

Gnomad SAS AF: 0.0806

Gnomad FIN AF: 0.00936

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0389

Gnomad OTH AF: 0.0542

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

GnomAD4 genome AF: 0.0611 AC: 9290 AN: 151994 Hom.: 435 Cov.: 31 AF XY: 0.0603 AC XY: 4476 AN XY: 74284

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0418

Gnomad4 ASJ AF: 0.0263

Gnomad4 EAS AF: 0.00677

Gnomad4 SAS AF: 0.0807

Gnomad4 FIN AF: 0.00936

Gnomad4 NFE AF: 0.0389

Gnomad4 OTH AF: 0.0536

Alfa AF: 0.0174 Hom.: 6

Bravo AF: 0.0641

Asia WGS AF: 0.0390 AC: 135 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	3.9
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7283476; hg19: chr21-31616101;