rs11004422

chr10-46097486-T-Cchr10-46097486-T-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 0.467 in 151,744 control chromosomes in the GnomAD database, including 16,796 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 0.47 (16796 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.597 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: 0.467 AC: 70827 AN: 151626 Hom.: 16765 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.467 AC: 70906 AN: 151744 Hom.: 16796 Cov.: 32 AF XY: 0.468 AC XY: 34712 AN XY: 74116

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.490

Alfa AF: 0.478 Hom.: 2348

Bravo AF: 0.463

Asia WGS AF: 0.535 AC: 1860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11004422; hg19: chr10-51498336;