rs11253478

Variant names:

• chr10-98907-C-T
• rs11253478

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 0.122 in 152,268 control chromosomes in the GnomAD database, including 2,000 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 0.12 (2000 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 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: 0.122 AC: 18532 AN: 152150 Hom.: 1989 Cov.: 33

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.122 AC: 18541 AN: 152268 Hom.: 2000 Cov.: 33 AF XY: 0.130 AC XY: 9679 AN XY: 74436

Gnomad4 AFR AF: 0.0278

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.109

Alfa AF: 0.138 Hom.: 335

Bravo AF: 0.126

Asia WGS AF: 0.331 AC: 1147 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	2.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11253478; hg19: chr10-144847;