rs10811474

Positions:

• chr9-21114238-A-G

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 0.444 in 151,760 control chromosomes in the GnomAD database, including 15,350 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 0.44 (15350 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 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: 0.444 AC: 67399 AN: 151642 Hom.: 15333 Cov.: 31

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.444 AC: 67453 AN: 151760 Hom.: 15350 Cov.: 31 AF XY: 0.444 AC XY: 32929 AN XY: 74184

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.624

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.489

Alfa AF: 0.447 Hom.: 31031

Bravo AF: 0.466

Asia WGS AF: 0.561 AC: 1952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10811474; hg19: chr9-21114237;