rs11245204

Positions:

• chr10-126876507-C-A
• chr10-126876507-C-T

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 0.339 in 152,034 control chromosomes in the GnomAD database, including 10,320 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 0.34 (10320 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 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: 0.340 AC: 51585 AN: 151916 Hom.: 10325 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.339 AC: 51574 AN: 152034 Hom.: 10320 Cov.: 31 AF XY: 0.331 AC XY: 24558 AN XY: 74282

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.368

Alfa AF: 0.442 Hom.: 29401

Bravo AF: 0.326

Asia WGS AF: 0.252 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.52
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11245204; hg19: chr10-128565076;