rs11007350

Variant names:

• chr10-29000102-C-T
• rs11007350

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 0.457 in 152,030 control chromosomes in the GnomAD database, including 16,635 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 0.46 (16635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07

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 = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69495 AN: 151910 Hom.: 16639 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.457 AC: 69501 AN: 152030 Hom.: 16635 Cov.: 32 AF XY: 0.450 AC XY: 33437 AN XY: 74292

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.482

Alfa AF: 0.524 Hom.: 38568

Bravo AF: 0.450

Asia WGS AF: 0.273 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0060
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11007350; hg19: chr10-29289031;