rs9305434

Variant names:

• chr21-30702893-C-T
• rs9305434

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 0.569 in 151,892 control chromosomes in the GnomAD database, including 24,864 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 0.57 (24864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.626 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: 0.569 AC: 86291 AN: 151774 Hom.: 24827 Cov.: 32

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.569 AC: 86379 AN: 151892 Hom.: 24864 Cov.: 32 AF XY: 0.564 AC XY: 41891 AN XY: 74238

African (AFR) AF: 0.570 AC: 23601 AN: 41410

American (AMR) AF: 0.636 AC: 9717 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2143 AN: 3470

East Asian (EAS) AF: 0.307 AC: 1581 AN: 5156

South Asian (SAS) AF: 0.619 AC: 2988 AN: 4824

European-Finnish (FIN) AF: 0.492 AC: 5184 AN: 10536

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39112 AN: 67902

Other (OTH) AF: 0.607 AC: 1282 AN: 2112

Alfa AF: 0.581 Hom.: 73455

Bravo AF: 0.579

Asia WGS AF: 0.518 AC: 1805 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.22
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs9305434; hg19: chr21-32075211;