rs11003231

Positions:

• chr10-52869614-G-A
• chr10-52869614-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 0.28 in 152,028 control chromosomes in the GnomAD database, including 6,522 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 0.28 (6522 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 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: 0.280 AC: 42553 AN: 151910 Hom.: 6520 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.280 AC: 42573 AN: 152028 Hom.: 6522 Cov.: 32 AF XY: 0.280 AC XY: 20787 AN XY: 74298

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.298

Alfa AF: 0.318 Hom.: 10322

Bravo AF: 0.274

Asia WGS AF: 0.306 AC: 1065 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	0.59
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11003231; hg19: chr10-54629374;