rs10488723

Variant names:

• chr11-110782369-T-C
• rs10488723

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 0.0413 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
• Publications: 1 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0165 AC: 686 AN: 41578

American (AMR) AF: 0.0293 AC: 448 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0673 AC: 233 AN: 3464

East Asian (EAS) AF: 0.0320 AC: 166 AN: 5194

South Asian (SAS) AF: 0.0290 AC: 140 AN: 4822

European-Finnish (FIN) AF: 0.0387 AC: 411 AN: 10618

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0585 AC: 3980 AN: 67978

Other (OTH) AF: 0.0402 AC: 85 AN: 2112

Alfa AF: 0.0558 Hom.: 143

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
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs10488723; hg19: chr11-110653092;