chr21-30243783-A-T

Variant names:

• chr21-30243783-A-T
• rs7283476

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.127 AC: 5262 AN: 41416

American (AMR) AF: 0.0418 AC: 638 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0263 AC: 91 AN: 3466

East Asian (EAS) AF: 0.00677 AC: 35 AN: 5170

South Asian (SAS) AF: 0.0807 AC: 388 AN: 4810

European-Finnish (FIN) AF: 0.00936 AC: 99 AN: 10576

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0389 AC: 2644 AN: 67984

Other (OTH) AF: 0.0536 AC: 113 AN: 2108

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs7283476; hg19: chr21-31616101;