rs11008222

chr10-30753565-G-Achr10-30753565-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 0.395 in 151,998 control chromosomes in the GnomAD database, including 13,027 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 0.39 (13027 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 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: 0.395 AC: 59947 AN: 151880 Hom.: 13019 Cov.: 31

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.395 AC: 59985 AN: 151998 Hom.: 13027 Cov.: 31 AF XY: 0.390 AC XY: 28967 AN XY: 74284

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.443

Alfa AF: 0.484 Hom.: 31771

Bravo AF: 0.389

Asia WGS AF: 0.398 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.37
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11008222; hg19: chr10-31042494;