rs11003231

Variant names:

• chr10-52869614-G-A
• rs11003231

Your query was ambiguous. Multiple possible variants found:

• chr10-52869614-G-A
• chr10-52869614-G-C

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 0.28 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.148 AC: 6122 AN: 41490

American (AMR) AF: 0.327 AC: 5000 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1861 AN: 5152

South Asian (SAS) AF: 0.309 AC: 1490 AN: 4820

European-Finnish (FIN) AF: 0.312 AC: 3295 AN: 10562

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22750 AN: 67946

Other (OTH) AF: 0.298 AC: 630 AN: 2112

Alfa AF: 0.315 Hom.: 12911

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs11003231; hg19: chr10-54629374;