rs1116470

Variant names:

• chr11-35072944-T-C
• rs1116470

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 0.503 in 152,080 control chromosomes in the GnomAD database, including 20,365 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 0.50 (20365 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.503 AC: 76448 AN: 151964 Hom.: 20361 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.503 AC: 76465 AN: 152080 Hom.: 20365 Cov.: 32 AF XY: 0.509 AC XY: 37810 AN XY: 74350

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.539

Alfa AF: 0.508 Hom.: 3760

Bravo AF: 0.499

Asia WGS AF: 0.684 AC: 2379 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1116470; hg19: chr11-35094491;