rs11253048

Positions:

• chr10-5219196-A-G

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 0.157 in 152,134 control chromosomes in the GnomAD database, including 1,925 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 0.16 (1925 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23818 AN: 152016 Hom.: 1921 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.157 AC: 23855 AN: 152134 Hom.: 1925 Cov.: 32 AF XY: 0.155 AC XY: 11525 AN XY: 74388

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.148

Alfa AF: 0.169 Hom.: 202

Bravo AF: 0.162

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11253048; hg19: chr10-5261159;