rs9305406

Positions:

• chr21-30013925-G-A
• chr21-30013925-G-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 0.735 in 151,896 control chromosomes in the GnomAD database, including 41,936 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 0.73 (41936 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371

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 (NFE) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111517 AN: 151778 Hom.: 41910 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.735 AC: 111593 AN: 151896 Hom.: 41936 Cov.: 32 AF XY: 0.729 AC XY: 54143 AN XY: 74248

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.745

Alfa AF: 0.795 Hom.: 83503

Bravo AF: 0.716

Asia WGS AF: 0.557 AC: 1937 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9305406; hg19: chr21-31386243;