rs10811474

Variant names:

• chr9-21114238-A-G
• rs10811474

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 0.444 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.419 AC: 17324 AN: 41380

American (AMR) AF: 0.555 AC: 8440 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1754 AN: 3472

East Asian (EAS) AF: 0.624 AC: 3215 AN: 5150

South Asian (SAS) AF: 0.550 AC: 2652 AN: 4818

European-Finnish (FIN) AF: 0.320 AC: 3374 AN: 10542

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.427 AC: 29008 AN: 67870

Other (OTH) AF: 0.489 AC: 1032 AN: 2110

Alfa AF: 0.446 Hom.: 44644

Bravo AF: 0.466

Asia WGS AF: 0.561 AC: 1952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.36
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10811474; hg19: chr9-21114237;