rs4938285

Positions:

• chr11-116569294-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 0.361 in 151,896 control chromosomes in the GnomAD database, including 10,277 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 0.36 (10277 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.35

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.116569294T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54798 AN: 151776 Hom.: 10264 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.361 AC: 54855 AN: 151896 Hom.: 10277 Cov.: 31 AF XY: 0.353 AC XY: 26227 AN XY: 74224

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.368

Alfa AF: 0.354 Hom.: 1978

Bravo AF: 0.368

Asia WGS AF: 0.309 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	20
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4938285; hg19: chr11-116440011;