rs10501483

Variant names:

• chr11-80894035-T-G
• rs10501483

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 0.0866 in 152,216 control chromosomes in the GnomAD database, including 1,731 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 0.087 (1731 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 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: 0.0866 AC: 13169 AN: 152098 Hom.: 1727 Cov.: 31

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.00684

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00326

Gnomad OTH AF: 0.0764

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

GnomAD4 genome AF: 0.0866 AC: 13187 AN: 152216 Hom.: 1731 Cov.: 31 AF XY: 0.0847 AC XY: 6305 AN XY: 74438

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.0410

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.0269

Gnomad4 SAS AF: 0.00684

Gnomad4 FIN AF: 0.0137

Gnomad4 NFE AF: 0.00325

Gnomad4 OTH AF: 0.0756

Alfa AF: 0.0395 Hom.: 220

Bravo AF: 0.0975

Asia WGS AF: 0.0400 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501483; hg19: chr11-80605078;