rs10488723

chr11-110782369-T-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 0.0413 in 152,272 control chromosomes in the GnomAD database, including 181 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 0.041 (181 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.057 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: 0.0414 AC: 6296 AN: 152154 Hom.: 181 Cov.: 33

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0293

Gnomad ASJ AF: 0.0673

Gnomad EAS AF: 0.0319

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0387

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0586

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0413 AC: 6291 AN: 152272 Hom.: 181 Cov.: 33 AF XY: 0.0393 AC XY: 2923 AN XY: 74466

Gnomad4 AFR AF: 0.0165

Gnomad4 AMR AF: 0.0293

Gnomad4 ASJ AF: 0.0673

Gnomad4 EAS AF: 0.0320

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.0387

Gnomad4 NFE AF: 0.0585

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0557 Hom.: 121

Bravo AF: 0.0415

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.046
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488723; hg19: chr11-110653092;