rs10501485

Positions:

• chr11-80933058-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 0.0458 in 152,220 control chromosomes in the GnomAD database, including 476 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 0.046 (476 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.80933058T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0458 AC: 6960 AN: 152102 Hom.: 475 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0231

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.0238

Gnomad SAS AF: 0.00393

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00268

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0458 AC: 6970 AN: 152220 Hom.: 476 Cov.: 32 AF XY: 0.0445 AC XY: 3309 AN XY: 74414

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0230

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.0238

Gnomad4 SAS AF: 0.00393

Gnomad4 FIN AF: 0.0138

Gnomad4 NFE AF: 0.00266

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.0296 Hom.: 40

Bravo AF: 0.0512

Asia WGS AF: 0.0330 AC: 114 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	0.27
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501485; hg19: chr11-80644101;